A long shot, but here's how I experienced similar symptoms: http://www.dovecot.org/list/dovecot/2016-April/104091.html
Kamil Madac wrote on 08/23/2016 02:02 PM:
Hi,
One of my email accounts has 1,5gb of emails in INBOX, but maildirsize shows only 528mb. 'du' also shows 1,5gb and there are 3809 files in cur directory.
When I use mailbox status a can see correct values:
doveadm -f table mailbox status -u user@domain.sk "messages vsize" INBOX* messages vsize
INBOX 3809 1521049349
but when I check the quotas with doveadm:
doveadm quota get -u user@domain.sk Quota name Type Value Limit % User quota STORAGE 541391 2048000 26 User quota MESSAGE 886
0
I tried to delete maildirsize, but it was recalculated again incorrectly.
2097152000S 554384829 886
Dovecot version is 2.2.9 installed from packages on Ubuntu 14.04 I have other accounts on server which are have no problems with maildirsize and quotas. Does anyone have same experience?
Kamil