So I frequently change files and ultimately I keep losing my way-points. Please take the time to add a waypoint.dat system that syncs between server and clients. Waypoints in the configs are impractical.

they need a way to sync ... so when someone for example accidentally overwrites a file then it is still there.

The file is only used by the server. The client does not need it. There is no syncing involved and the client can overwrite as many files as it wants. The only issue is when it comes to overwriting the config file on your server (e.g. when lazy-updating a pack) in which case yes, having a separate file for the global waypoints would be good. But it has nothing to do with syncing.

The waypoints in the config file have nothing to do with the client. Normal waypoints are stored in player data. The config ones are only for global ones on servers.

Yeah when you update a mod-pack everyday 2 or 3 times a day you decide to cut as many corners. Thank you for understanding my situation though!

Why you don't store this information in the world directory?… This makes config unportable.

This was fixed a year ago.

"In next version."
I got it.