In After Effects, I often get an error message about an unsupported format. This error usually occurs for MP4 and SWF. I converted both to MOV (it works mostly), but when I open the file again, it shows the error message again.
Where your files are stored? Are they stored in a folder that is synced with the cloud (Google Drive, DropBox, etc)? If yes, try importing them from a different location and see if that brings any change.
Where your files are stored? Are they stored in a folder that is synced with the cloud (Google Drive, DropBox, etc)? If yes, try importing them from a different location and see if that brings any change.