I couldn’t figure it out; very irritating.
But, i did find a way to beat the system. Set your Pedal settings, remove SD card and put into your PC/Mac. Next, open the SD card in the ‘Explorer/Finder’ and look for the PARAMS folder. Copy it to a backup folder on your local PC/Mac.
Then each time you do anything in BB Manager and export back to your SD card. Copy your PARAMS backup that you made earlier back on the SD card (overwrite the PARAMS folder.)
Also, this way you could, if you chose to, make different PARAMS settings backups.