Hello,
I also got hit by this bug - old mailboxes were still in the place, but
new empty mailboxes started to appear in uuid folders. And mailboxes.db
got corrupted/erased.
The easy way is to add to /etc/imapd.conf
mailbox_legacy_dirs: yes
BEFORE starting the upgrade. See:
https://www.cyrusimap.org/3.6/imap/download/upgrade.html#storage-changes
So the easy way would be to add this information to NEWS.Debian.gz
More complicated (but more secure) way, would be to add this option
automatically if upgrading from version < 3.6.0
--
Best regards
Vladislav Kurz