I just tried it - I added a drum kit to the project and did a ‘Save’. The footswitch settings didn’t change. I also opened the project from my computer, made some changes, then did a ‘Synchronize’. The footswitch settings didn’t change. I also exported the project from BBManager to the card which appears to do a complete overwrite and the footswitch settings didn’t change even though I made a change to one of the settings in between.
BTW, I have firmware version 1.74. Maybe the engineers fixed this problem in the upcoming firmware update. That would explain the differences in what we’re seeing.
Somewhere along the way with this morning’s experimentation, my settings did get changed but not all the way back to factory. The best I can tell you is to get the settings the way you want on the pedal, open the project from the card, then save that project to your computer. Same for any other projects you have. See if that gets the footswitch settings retained in your computer in sync with the ones on your card. That seems to work for me.