That's why it is emphasized in the readme --> Manually SAVE OFTEN!
It would also be a good idea to turn on Aurora Savegame Protection in case you need to go back to a previous save.
the trainer must work fine if there is no update requests. There needs to be at LEAST *3* update requests for the trainer maker to look into an issue.
Please use the update notification system to report a game patch, update or to report that the trainer may not be working with the latest version of the game. If 3 or more reports have been filed, consider BOOSTING the priority of this title for a faster turnaround on the updated trainer.
Add you save game for this. Sounds like a very specific issues that most likely didn't show when trainer was made.
Only fix would be to have your save game with the items that disappear so that trainer maker can have a look.