Yes it is - it is simply not calculating the folder size correctly. I don't know if this an underlying OS issue (32-bit vs 64-bit), or a TB bug...
Ahh, you were right about this, I did see later that all the messages *were* there in fact, but it does "loop" the folder size as was stated (6G looks like 2G in TB, etc). I appreciate all the info from everyone, and I was able just to just move all of the 40G around using Thunderbird once I saw that all the messages were indeed there. Took a while :), but now we have some things archived and folders are down to a more "reasonable" size (reasonable for us anyway).
It is good to know that removing messages directly from the source folders won't mess up anything as far as Dovecot or its indexes is concerned though, so, thanks for that information everyone!! Dave