I know we went over this in the ticket. But for others that are having the same problems.
Personal annotations are held by your character. They should stay no matter what happens. Village annotations are held by the village you are a citizen of. If you change Village these will be erased/changed to whatever the new deed has marked. In PvE alliance annotations are held by the Capital of the alliance. Any time the Alliance Capital is changed, alliance annotations will also change.
All that being said when we first started playing on the new servers. When you press M it brought up map that showed all the servers in our current cluster. This was changed semi recently to just show the map you are on. when that happened I lost all my map annotations also. I don't know if this was intended and or the way it had to work.
If your annotations are currently still being removed on seemingly randomly on login and then come back and disappear again then please add as much information as you can so that the bug trackers can try to reproduce it.
The low res map for me stayed into I did a forced verify again on my packs. https://prnt.sc/trvy59
Hopefully we can track down this annoyance of your map annotations disappearing.