Found a fix! From a 2+ year old post …
Ok, so I’ve followed Blizzard’s UI resetting guide and found out that the culprit was within WTF folder. To avoid loosing all settings I’ve played a detective and narrowed it to WTF/Account/“acc name”/Server/“char name”/config-cache.wtf file. Deleted the line:
SET trackedAchievements (and whatever was after it)
and my tracker was finally empty.
Writing this in case someone runs into similar problem in the future.
This fixed my missing achievement tracker AND the quest tracker.