I ran into that with the map file downloads, too. When I saw that world.exe was considering ALL of the pre-installed map files "out of date" and was re-downloading them individually, I cancelled the download process. Reloading world.exe afterwards allowed the server to come up, since the database portion had been properly marked as being up to date.
The red icon on the Maps folder is the Git software indicating that files were added from some other location besides Git, so it can't vouch for them. Would indeed be safest to do a git pull on them to be sure everything's kosher.
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