Interesting Mbox / Maildir

How would it be possible for a cpanel system to "convert" from maildir back to mbox without direct intention / invention?

The story

1) Mail (with mailscanner - maildir) works fine for months - Exim failed and don't want to restart

2) Contact support company - Fixed and restarted exim

3) No email for 30 hours - Techs checked, tested, removed mailscanner and confirmed everything works fine

4) Found the problem myself - Email system still on maildir but exim delivered mail to INBOX folder instead than the maildir folders so I fixed it by running the maildir conversion to move the mail in inbox to the correct maildir folders.

5) The server support company insist that THEY did not break the system and everything working fine etc but I am sure that I am correct.

a) Stopped to receive any email direct after their tech fixed the exim issue. (After I did the conversion I got over 400 emails, the first of them the email from them that said exim is now fixed and restarted)

b) They created test email account and confirmed with tests that everything works fine but I think that the newly created email account would be a MBOX account and thus working fine while the rest of the email accounts on the server would still be maildir accounts and thus not receiving any emails until I ran the conversion script.

I am no server admin or tech so I cannot say what error would turn mailbox back to mbox hence the question above.

(Important - It worries me a bit as to why exim failed in the first place and while the first mail I received from the techs sort of "proof" that something they did caused the backwards conversion it's also possible that something else such as an automatic update caused this - Since exim failed I would not receive any mail at all, and after the tech restarted exim their email would be the first to land in the inbox instead of maildir folders)

Maybe worthwhile to investigate the reason why exim failed and what caused the turn from maildir to mbox because I think it would then be a global cpanel issue.