Emails in Thunderbird disappear on repair

Question

I have a (large) number of strangly corrupted local folders in Thunderbird. As far as I am aware, all emails in these folders are currently displaying correctly. They are shown in the folders, and I can open them and read them. However, all or almost all emails in these folders disappear if I apply any of the following operations to the containing folder:

• repair folder (context menu > Properties > Repair folder)
• export folder as mbox-file and reimport it (using ImportExportTools addon)
• close Thunderbird, delete *.msf file associated with the folder, and restart Thunderbird

(I've also tried migrating the folders to Evolution, in several different ways, but this is perhaps a different story. The best result I have been able to obtain is equally strange: I can see the migrated emails on the disk, but Evolution displays the folder as empty.)

Does anybody have an idea what might be going on? Is there a way I can “repair” my folders without losing my emails?

system:        Ubuntu 14.04
software:      Thunderbird 45.3.0

Account Settings 
  > Local Folders 
    > DiskSpace: 
      Don't delete any messages.
    > Message Storage Type:  
      file per folder (mbox)

Answer 1

I have, meanwhile, found two ways to restore these folders to a state in which they are stable under the operations described in the question:

Option A: move folders to an imap server & back (using drag & drop)

[Initially, I had incorrectly reported that this does not help. But this was because I had inadvertedly been using a pop-server and other local mail storage instead. Sorry.]

Option B: export & reimport emails as eml-files (using ImportExportTools addon)

[This option I had already reported on in my original question, but it has several drawbacks:
(a) I need to do this for each folder manually,
(b) Marking emails as read is no longer functional after this process: they are sporadically reverted to “unread“ status. In particular, all emails get reverted to “unread” status when I “repair” the folder.]

If anybody knows what is actually going on here, and how the problem is “supposed” to be fixed, I’d still be interested.