ok i fixed the above issue with the material not having a texture (which should not be issue since some materials will not have textures since they are just using color for example) and reverted things, moved the folder back manually (wish revert did this) and did combine again and this time got lot of different errors

Mesh.vertices is too large. A mesh may not have more than 65000 vertices.
UnityEngine.Mesh:set_vertices(Vector3[])
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:361)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Mesh.colors is out of bounds. The supplied array needs to be the same size as the Mesh.vertices array.
UnityEngine.Mesh:set_colors(Color[])
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:362)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Mesh.normals is out of bounds. The supplied array needs to be the same size as the Mesh.vertices array.
UnityEngine.Mesh:set_normals(Vector3[])
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:363)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Mesh.tangents is out of bounds. The supplied array needs to be the same size as the Mesh.vertices array.
UnityEngine.Mesh:set_tangents(Vector4[])
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:364)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Mesh.uv is out of bounds. The supplied array needs to be the same size as the Mesh.vertices array.
UnityEngine.Mesh:set_uv(Vector2[])
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:365)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Failed setting triangles. Some indices are referencing out of bounds vertices.
UnityEngine.Mesh:set_triangles(Int32[])
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:366)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Material doesn't have a texture property '_CubeMap'
UnityEngine.Material:GetTexture(String)
MadMeshCombiner.ObjectGroup:<CubeMapTextures>m__B(GameObject) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
System.Linq.Enumerable:ToArray(IEnumerable`1)
MadMeshCombiner.ObjectGroup:CubeMapTextures() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:239)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Material doesn't have a texture property '_CubeMap'
UnityEngine.Material:GetTexture(String)
MadMeshCombiner.ObjectGroup:<CubeMapTextures>m__B(GameObject) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
System.Linq.Enumerable:ToArray(IEnumerable`1)
MadMeshCombiner.ObjectGroup:CubeMapTextures() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:239)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Material doesn't have a texture property '_CubeMap'
UnityEngine.Material:GetTexture(String)
MadMeshCombiner.ObjectGroup:<CubeMapTextures>m__B(GameObject) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
System.Linq.Enumerable:ToArray(IEnumerable`1)
MadMeshCombiner.ObjectGroup:CubeMapTextures() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:239)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
Material doesn't have a texture property '_CubeMap'
UnityEngine.Material:GetTexture(String)
MadMeshCombiner.ObjectGroup:<CubeMapTextures>m__B(GameObject) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
System.Linq.Enumerable:ToArray(IEnumerable`1)
MadMeshCombiner.ObjectGroup:CubeMapTextures() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:518)
MadMeshCombiner.MadMeshCombinerTool:Combine(String, ObjectGroup, Transform) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:239)
MadMeshCombiner.MadMeshCombinerTool:RecombineManaged(MadMeshCombinerManaged) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow:CombineManaged() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow:Combine() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow:OnGUI() (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
UnityEditor.DockArea:OnGUI()
NullReferenceException: Object reference not set to an instance of an object
MadMeshCombiner.MadMeshCombinerAtlasBuilder.CreateItem (UnityEngine.Texture2D texture, Rect region) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerAtlasBuilder.cs:194)
MadMeshCombiner.MadMeshCombinerAtlasBuilder.PackTextures (UnityEngine.Texture2D[] textures, System.String path, System.Collections.Generic.List`1& items) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerAtlasBuilder.cs:170)
MadMeshCombiner.MadMeshCombinerAtlasBuilder.CreateAtlas (System.String texturePath, UnityEngine.Texture2D[] textures) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerAtlasBuilder.cs:91)
MadMeshCombiner.MadMeshCombinerTool.Combine (System.String directory, MadMeshCombiner.ObjectGroup group, UnityEngine.Transform parent) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:258)
MadMeshCombiner.MadMeshCombinerTool.RecombineManaged (MadMeshCombiner.MadMeshCombinerManaged managed) (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerTool.cs:100)
MadMeshCombiner.MadMeshCombinerWindow.CombineManaged () (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:118)
MadMeshCombiner.MadMeshCombinerWindow.Combine () (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:103)
MadMeshCombiner.MadMeshCombinerWindow.OnGUI () (at Assets/Mad Mesh Combiner/Scripts/Editor/MadMeshCombinerWindow.cs:84)
System.Reflection.MonoMethod.Invoke (System.Object obj, BindingFlags invokeAttr, System.Reflection.Binder binder, System.Object[] parameters, System.Globalization.CultureInfo culture) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Reflection/MonoMethod.cs:222)