You are right, 6GB would not cause that kind of problem.

I do not know about jemplode, but I do know that emplode would cause you trouble (inability to sync files) from the moment you cross that magic FID line. Even if you remove files afterward, you will still have trouble. One or two drives should not have mattered.

The symptoms I remember were that I could sync, loading lots of files, but that emplode would crash when it attempted to rebuild the database. This forced a manual database rebuild each time, but not necessarily a full fsck.

I am not convinced this is your problem, but it could not hurt and it is similar enough that it might be. Another thought is to sync with emplode / jemplode, but leave a console link open via serial and watch for any console messages or errors.