Installed following mods:
Map Atlases - 1.20-6.0.16
Map Atlases + Waystones Compatibility - a2w-1.0.0
Supplementaries - 1.20-3.1.31
Moonlight lib - 1.20.2.14.11

In my modpack im playing, Dawn of the Flood, I installed the mods above. I also often make backups, but after using said backups, all the markers except waystones and beds disappear. I do the backups manually, though no backup mods installed.

Any idea how to prevent those markers from disappearing again?

edit: I now see that there is an error loading in the markers:
[Render thread/ERROR] Could not load client markers saved data at USERSDIR\instances\DawnoftheFlood\map_atlases\singleplayer<worldname>.nbt

Any way how to prevent that from happening because that is what I assumed was the problem at first also.

Well as long as the file matches the world it should be fine. All the data is just there afterall

It should though, I think,

I copy the folder and name the folder like " - 5" and when I want to go back to an older world I place that folder, remove the current world and then rename that folder to "". But I guess there is still something different that the mod doesn't like then.

Well the data is all there and in the world (which includes the save data where the map is saved). There's no other file where that is stored so restoring a saved version of both Vs loading up a world is virtually identically as far as the game is concerned. Double check everything

Both files have to be identical btw

That's because you are likely not copying the map atlases folder or that data became invalid