The user can check if the repository of their project is corrupted, by going to the top menu > Paratext column > Advanced > Diagnostics > Verify repository.
If this check says the repository is corrupt, the best thing to recover is to delete their copy of the project and get a new copy of the project from the server.
Since they were in the process of making changes they have not shared, they can make a backup to file of the project, then restore from that file into a temporary new project, then delete the shared project and get a new copy of the shared project. Now they can copy their changes from the temporary new project and paste into the shared project.
But if they are typesetting, they should follow the typesetting options mentioned on this page: