mails are in the folder but not appearing on TBP

Hi.
I'm just fiddling about with my ThunderbirdPortable and I looked into the files in my "Data\profile\Mail\Local Folders". There are the small .msf files and bigger files wwith the same name. I already learned that the .msf files contain TB's information about the mails in the bigger files. In some of the bigger files I can read old emails I already deleted and I'd like to delete them completely because they need pretty much storage space.

I already tried to delete the .msf files and restart Thunderbird but I still can't see the old messages on TBP to delete them again. How can I do this? (I could probably delete them by hand using the editor but that would be a lot of work...)

background:
I only realised this because I could not start TBP again after the update to version 2.0.0.17 that TBPortable had suggested me. That's why I completely reinstalled TBP and copied a backup of the profile folder into the new version. Maybe I missed to copy something crucial because I had an access denied file (a broken folder which I could not delete in TBP itself) in the folder that stopped the copy process when I created the backup. (I know for example that I did not copy the extensions folder and had to reinstall my add-ons). I also did not copy the access denied file back to my new TBP setup again.