Hi,
This is common to happen when script compilation fails and we are trying to find a way to make sure this does not happen. Some work has already been done Addressing issues with missing references
The recommend fix is to handle all compilation issues and then force reimport all prefabs, simply right click in the project browser on prefabs. Might be fastest to type t:prefab
in the search bar and select all prefabs to make sure all are reimported.
I hope this solved your issue
Don’t try to recreate your prefabs like you mention above, this will change all GUIDs and probably cause even more problems