Did you also take a look at this portion of Potential MineOS Web UI Lag Fix for Dynmap users
I think you may also be able to specify a location that is outside of the server directory, which if switching to sqlite (as well as manually deleting all of the existing map files within the Dynmap map directory - whatever that directory is named/called, you should know pretty instantly as you’ll see tiles of different parts of your Minecraft world/the map within it - within the server’s directory) doesn’t fix it for you then maybe moving that file someplace else that is completely outside of the main base servers directory then pointing Dynmap to it; example commands and configuration below:
mkdir /var/games/minecraft/dynmapdbfiles
storage:
# Filetree storage (standard tree of image files for maps)
#type: filetree
# SQLite db for map storage (uses dbfile as storage location)
type: sqlite
dbfile: /var/games/minecraft/dynmapdbfiles/server.db
Again please do not just simply copy and paste these but use them as reference.server.db , you ideally would want to change this to something per-server, such as matching your server names exactly for example. One thing to note is going this far will also exclude the dynmap sqlite db files from backups and archives, as well as restores, though dynmap should end up updating it anyways and it likely isn’t really anywhere as important as the actual server itself so no big deal I’m sure.
If the sqlite db file is still in the server directory MineOS may still hang up on it due to it’s file size which is why having it outside of a watched/monitored MineOS directory would be best, like the one in that example.