When I start the server with this markers.yml: markers.yml.original.txt
It soon is regenerated almost empty: markers.yml.result.txt and my markers are gone.

Running latest Paper and Dynmap versions. Any help appreciated.

If using MySQL the markers are stored in the database

I‘m using flat files.

Then it's probably not liking the format, please add the markers using commands instead of the files

Then it's probably not liking the format, please add the markers using commands instead of the files

All markers were added using commands.

I couldn't get a test case to work to figure out the problem, so I ended up starting from scratch. Maybe some additional logging on debug level would help.

I'm not sure, but i think enabling debugging shows what gets loaded when