On some file systems 2 GB is a hard limit. Furthermore big files with lots writing actions are easily corrupted.
That your inbox didn't decrease in size is because TB doesn't really delete messages, but marks them as deleted. (TB isn't alone in that, almost every mailclient and database application does the same.)
To really remove the messages you need to compress the message base, that's an action you can do manually with TB or automated on exit or via the scheduler. When you do this on exit, you can set to compress all folders (in the account settings) or only specific folders (in the folder properties)
I suggest to do this on exit for all folders:
account -> properties -> options -> compress all folders on exit.
I also advise to do it the first time manually:
Select the inbox and via the menu choose:
Folder -> Purge + Compress
This way you'll get a pop-up that shows you how much space you recovered.
__________________________________
I'm just a user of The Bat! I don't work for Ritlabs.