I appreciate the help of you all, but sadly that doesnt help get the missing mails back.
I have contacted Avast via report false-positive section and MartinZ here in forums, as he seems to work for the company. So far I got no answer.
I like my backups local and not in the cloud or on a server somewhere. And that works pretty well. In this case I had to move the primary backup temporarily for privacy reasons, not realizing Avast! would simply destroy every instance of the Inbox it came across. I use Thunderbird for over 10 years now and before that I used MS Outlook. Until now I never lost any mail.
@stibi: Yes I have two older instances of backups. But Im still missing a third of the mails. Its not just the amount, things like this simply should not happen.
@DavidR: my report folder only has aswBoot, BehaviourShield, EmailShield, FileSystemShield, WebShield. In the Scan-History its still there, dunno where its saved. I took a look at the index of the chest and it really only shows the 3 older false positives from some games.
Digging in the files a bit, log of chest shows
14.04.2018 11:59:58 Error 112 in s_NewFile
14.04.2018 11:59:58 Error 112 in chestAddFileRpc
14.04.2018 11:59:59 Error 112 in s_NewFile
14.04.2018 11:59:59 Error 112 in chestAddFileRpc
14.04.2018 11:59:59 Error 112 in s_NewFile
14.04.2018 11:59:59 Error 112 in chestAddFileRpc
Well, destroyed everything in 2 seconds. And from what I can see that happened after I stopped the scan, so if the list/button would have worked it might have been avoidable