Problem

After a successful bulk migration from one Mattermost Server to another, some users' channels are not correctly marked as unread, and notifications appear to be intermittent.

Solution

While a fix for this is already in active development, this issue occurs due to a mismatch in imported and real data on the system.
As a fix, the following SQL query can be run on the affected Mattermost Server's Database.

UPDATE ChannelMembers
SET 
msgcount = channels.totalmsgcount, 
lastupdateat = channels.lastpostat, 
lastviewedat = channels.lastpostat,
msgcountroot = channels.totalmsgcountroot
FROM channels
WHERE channelmembers.channelid = channels.id;

After running this query, all channels will be marked as read, so make sure to either run it as soon as you finish the migration or give your users a heads-up before running it.

This issue should be resolved with Mattermost 10.1 (exact fix-release may change, but this article will be updated to reflect this).