I suspect it keeps the SD card in ‘sync’ with the project files in the manager, but couldn’t find a good explanation in a forum search. I get a prompt every so often about being able to synchronize projects. Not sure if it performs a synchronization automatically or it’s a manual sync or if I really need to enable this at all. Not knowing how it exactly works I’m not sure if it’s possible to accidentally overwrite data on the SD card.
It’s supposed to be a bi-directional process, in other words, when you sync your BBM project it coordinates song edits, deletions and additions from your BBM project with the project on your SD card; if you’ve made changes to any beats or songs (tempo) on your pedal as well as pedal settings, it will synchronize them with the BBM.
I never get a prompt to synchronize my BBM project to my card but that may be a function of how poorly the BBM Synchronize Project to SD Card behaves under my Mac OS (High Sierra). The process is supposed to be user controllable using the BBM and should not be automatic. Does it happen when you save your project in BBM? Bottom line is Synchronization should be a manual process.
Export > Project to SD Card is different in that it is a one-way data flow from the BBM to the pedal. It will prompt you that a project exists on your SD card and ask if you want to overwrite it. It will not sync your pedal settings—in fact, it overwrites them, forcing you to reset your pedal settings when the export completes.
If I recall the prompt comes up with a message similar to I think when saving, ’ Do you want to be able synchronize future projects - Y/N?’ I’ll have to give some thought as to what may work best for me. My pedal settings got overwritten a while back when I loaded a new project and I couldn’t figure out why, but now I know. I had thought the pedal settings were independent of the saved project, but evidently not.
Hope I’m not going to confuse you too badly with the following: 
If you have opened a new project or renamed a project using the BBM Save Project As . . . and you save and then export to SD card, it will cause this prompt.
If you are Synchronizing a project to your SD card that you have previously synchronized, you should only get the prompt the first time. You could also get this prompt when you are using two SD cards as a primary and a backup. When you try to sync the primary and then the backup, one of the two may not be synchronizable.
There is a semi-automated way to replace your pedal settings when you export a project to your SD card:
[LIST]
[]make sure your pedal settings are updated on your pedal the way you want them
[]power the pedal down and remove the SD card; place the SD card in your computer SD slot reader
[]navigate to your SD card and copy the PARAMS folder; paste to your desktop
[]once done and from your BBM > Export > Project to SD card
[]when complete, copy the PARAMS folder from your desktop and paste to the top level of your SD card and okay when prompted to replace; eject the SD card. You’ll only have to follow these steps when you update your pedal settings again
[]this should work—if it doesn’t, let me know
[/LIST]