Thunderbird unable to update folder changes on mailserver

One user (a boss) is using Thunderbird as his mail client and is the only one who does. The mail server is Communigate 5.3.
He accidentally moved his 2010 mail folder into another folder and lost it. In this 2010 folder there are subfolders, Out Q1, Q2, Q3 and In Q1, Q2, Q3, Q4.

I found his mail and moved it back up one level to the other 2008, 2009 folders using the Mail.app. Thunderbird showed the 2010 folder but not the content, the subfolders. Mail.app sees everything and sees all the mail in the subfolders.

I have tried to do this again by making a 2010-2 folder and move everything again. Tried to use Terminal mv to move the mail on the  server. The situation now is that Thunderbird sees some subfolders in 2010 folder and some in 2010 (which I have deleted) and since the trouble started there is also one italicized folder with the name "... does not exist" bah! And still three of the subfolders can not yet be seen.

I have done all these exercises on my mac and I just now set his Thunderbird account on a computer that has never even been touched by Thunderbird. I have used version 5.x and 6.0 to do this.

So it's quite clear that there are no files or cache on the client computer to delete since the untouched one is seeing the same stupidness.

I have also compared the privileges on missing and shown mail and it's the same on all: system and wheel r+w, everyone: no access.

I am running out of ideas how to fix this and need some expert to magically solve this.

Plan B: He has Mail.app on his mac and could use it to investigate this 2010 mail but I rather clean up this problem