Syncing to SD card question

Because of all the problems with BBM on my Mac I loaded my SD card into a Windows computer. I made some changes to my project and now I want to sync it back to the SD card but BBM is asking me what folder on the card I want to sync it to. It never did that before. How do I get it back to asking if I want to sync the project to the card?

When it prompts you for the folder, use the Explorer to navigate to the root level of the SD card and select that.

When I do that is says “Destination project at the file is not linked. Use File>Export>project to SD card instead” This is why I stopped using my Mac, when you do this export it blows out all your pedal settings. Is there a way to link the project to the SD card?