Well it definitely sounds like the backup file is fine. It shouldn't make a difference whether her library is empty before doing the restore. The database tables are fully populated after the initial load.
There shouldn't be an issue with going from v3.9 to v4.0, or any newer version for that matter. The database in the backup file is upgraded to match whatever version is current. Going from a newer version database to a lower version database could potentially cause issues though. I don't really have downgrade code implemented at the moment. If there was some critical error during this process, an error message would have been displayed. I'll continue looking for possible reasons for this issue. Obviously if I had a copy of your backup, I could debug the code while restoring it to try and track down issues. If this is something you are willing to do, let me know, otherwise I will keep digging on my end.
Is it possible for you to upgrade both tablets to v4.0.1 and try again? It would help eliminate any possible errors due to versioning, even if theoretically there shouldn't be any.
There shouldn't be an issue with going from v3.9 to v4.0, or any newer version for that matter. The database in the backup file is upgraded to match whatever version is current. Going from a newer version database to a lower version database could potentially cause issues though. I don't really have downgrade code implemented at the moment. If there was some critical error during this process, an error message would have been displayed. I'll continue looking for possible reasons for this issue. Obviously if I had a copy of your backup, I could debug the code while restoring it to try and track down issues. If this is something you are willing to do, let me know, otherwise I will keep digging on my end.
Is it possible for you to upgrade both tablets to v4.0.1 and try again? It would help eliminate any possible errors due to versioning, even if theoretically there shouldn't be any.