We are encountering a problem developing a tool that it suposed to edit custom keyframes of an animation, but we found out that there is no information about this neither on unity forums or unity documentation. Is there really a way to do it?
You can edit keyframes, yes, though afaik only at edit time - not during gameplay.
Is this in imported .fbx files, or in Animation files built in Unity?
To edit Animations, you use the AnimationUtility class. If they’re in an fbx file, you have to use the ModelImporter to get the data and modify it.