I've seen many people posting about issues with the Bonus playlist from Yamaha. I've had the same issues and figured out a solution that works for me. While I can't reference a particular post on here that pointed me in the direction - it was the cumulation of reading on here plus YT videos - and I'm super grateful for all of that.
In short - I've given up on the playlist itself and I just use the registrations.
I simply copied the registrations themselves from the USB to the User section in a new folder I called Bonus List, then I removed the USB. Once the indexing caught up, I could search within the registrations sections for any of the songs. If I go to the Playlist section there is nothing there. This works for me because I'm not gigging. Personally, I start with the sheet music to a particular song, then look for a registration to go with it as a starting point, then adjust to my taste.
Fred pointed out that if there are any styles that came with the bonus playlist, those would be on the USB and the registration would go looking for them, and not find them. (big thank you to Fred for all of his contributions and help!). So far, I haven't been through every song, but so far I haven't found anything that doesn't work.
Here's the video that others have linked to that Yamaha did on getting the registrations -
https://youtu.be/Tqa7x62Zt4IFor me, the breakthrough moment was realizing that the playlist is simply a list referencing registrations. If I have the registrations themselves, I don't need a separate list, meaning I don't need the playlist function.
This has allowed me to avoid the issues of which USB is in 1 or 2, having it out because I'm using a different one etc.
Hope this is helpful to others.