Multi-file Migrations With Renaming are Failing
If your solution has many files and you are doing migrations that require renaming the files, please be aware that neither Otto nor the FMPMigrator can update the file references between those files. Only the FileMaker Advanced Developer Tool can do that. In this case the migration will work just fine, that is the data will be transferred, but since the File References are still pointing at the old files, it will appear as though it did not.
This is common use case for people who have vertical market solutions and are hosting many copies of their solution on a single server. Each copy has a different file name pattern. Doing a data migration will require renaming the files to match that File Name pattern.
The solution is to update the File References after the migration manually. OR even better, use variables to define the File References between your files so they can dynamically find the right files when they open.
You can read up on how variable file references work in FileMaker help document on Editing FileMaker data sources.