I don't understand... what is the relation between battery showing 0% (even if charged) with the alarm system?
I just had the same issue recently.. removed cable, stopped/started multiple times, nothing... battery was flashing and showing 0%.
But I knew the battery level was ~60% and I started to ride. After 2-3 minutes after started to ride, the battery recovered and showed the correct percentage, but after few seconds showed again 0%, then recovered again... and so on... after 3-4 such cycles it worked and showed correct percentage.
Now it seems to work... but I wonder: is it a sign of deadful battery, or the communcation with BMS? Does it have sny relation with temperature? (my TC stayed outside at below 0 degrees for few weeks, not moved, of course with the battery removed and kept inside the house)