missing emails in mutt

I'm using mail/mutt and mail/isync for many years and have never noticed any issues. However, today I missed an email (which I found via the web interface) and decided to investigate the situation.
I run mbsync via cron, it's using IMAP, so all boxes are in sync, I do not use mail/procmail or any other mail processing programs: the mail goes directly to the boxes. My home computer has 6 messages more than my work computer (out of ~7700). Today I copied all config files from one to another and ran mbsync – nothing has changed!

Thanks for troubleshooting ideas!
 
In the past I have started using FreeBSD I have had issues using the mbox format. Mails have been copied to /var/mail/USER instead of beeing processed by mail/procmail. The solution for myself has been to convert everything to the maildir format. This is just because you mention boxes. I have no idea about IMAP and if it works with mbox. The reply is more or less a shot in the dark. I hope you will fix that issue!
 
The solution for myself has been to convert everything to the maildir format. This is just because you mention boxes.
I'm using only maildir. I hate huge mbox files. "Boxes" are directories for IMAP channels.
 
What "web interface" are you referring to?
My service provider's web interface, doesn't actually matter, I did get that message in my home computer, but not in my work computer.
Did you try a grep -R search on your local Maildir directory structure
Yes, I did. Also, even if it was moved somewhere, IMAP would synchronize all clients, right?
The thing is it's not just one message, I'm missing 6 from different times in the same mutt's directories.
 
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