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I don't know what you've tried, but these are the steps I would take.
1. With the project open in RH, open the baggage files directory in the project explorer and delete any that don't belong there. RH may or may not do this, and even if it does seem to delete them from the project, it leaves them in the project folder.
2. With project closed, open the project folder and delete any that don't belong.
3. With the project closed, launch MS Access and open the project.cpd file.
Under "Tables" you'll see BaggageFileList and BaggageFileReferences.
4. Open BaggageFileList and study its contents. Are there duplicates? Are files listed that you "threw away" a long time ago? It is safe (assuming you have backed everything up) to delete lines from this table, and RH probably will forget they were ever there.
5. BaggageFIleReferences shows links from topics to baggage files. If a file is referenced only in the TOC, it's not listed here.
The Baggage File ID corresponds to the ID in the BaggageFileList table. You may have some entries that don't make sense -- references to topics that don't exist any more in the file table.
6. The Topic ID in the baggage references table table corresponds to the Topic ID in the Topic List table. Are there entries in the references table to topics that don't exist in the project?
After you save the revised database (by the way, consider running a database Compact and Repair from the Access Tools menu), open it the project in RH and see what's in the project directory.
I don't know how the rhbag.apj file fits in -- whether RH rebuilds it according to the CPD tables, or it has a life of its own and somehow informs the WebHelp generator. So you may have to work on this file after you clean up the database.
I hope this helps.