So, most of the time I work from my computer, setting setlists, charts and whatnot. Yesterday morning, loading my car for a show, I open my pedal-board case, remove the SD card from the BeatBuddy just to add 2 new songs that I wont even play today. Sync, eject, re-insert in the BeatBuddy : No song. 
Repeat the process religiously. Still No song. I got to go now so, reach for the family camera SD card → sync with the BeatBuddy Manager and voilà . The BB now works perfectly. But wait, Playlists ! I use playlists extensively (recalling 187 songs through MIDI) no way I can set that up in 5 minutes. I now realize I have to backup the PLAYLISTS folder and cannot rely on the Manager (I should have known that though as it is an explicitly unsupported feature of the oh so comprehensive BBManager).
Install my gear at the venue : No song. Get some random laptop to figure out what is going on with the SD card. Seems to be corrupted. No clue what so ever. Try everything while chairs are filling up. Did 2 hours of show without a single note from my BeatBuddy.
Back home: reformat all cards, re-sync, etc. The BB is now working. Three reboots later, still working. I wish I never go through that ever again. If only I could somehow know what went wrong. It is for now a random thing that can happen and is added in my morning prayer for the lord to save me from another no-drummer-show.