m ore likely an indexing issue in Thunderbird showing a no longer present thread.

See https://support.mozilla.org/en-US/kb/rebuilding-global-database

Rebuilding the global index may well make it disappear from results as the index is updated to reflect available emails. It might also make the original appear, but usually they simply disappear from the stale index and search results.

By chance I moved the folder that I suspected the email was in, from my archive back into my Inbox. And voila the who thread reappeared. Problem solved. @Matt, thanks for the reply and suggestion. Guess it was indeed a indexing issue that solved itself when the email I was missing was in fact placed back in the location the search said it should be in.

Martijn,

Is the archive in your imap account? Or is the archive in Local Folders?

It was in my local folder. The issue solved itself when I moved the folder back in my imap inbox

Not finding a message in Local Folders with Search is this bug https://bugzilla.mozilla.org/show_bug.cgi?id=1205248

Martijn,

Can you test this please...

If you move a single message at a time, do you see the same problem?

In other words, does moving multiple messages have a different result than moving a single message?