Sometimes display arrangement with three monitors messes up after returning from sleep. AtIs it possible to make a backup of layout?
You could back up ~/.config/kwinoutputconfig.json and try restoring that when things get messed up?
when i change refresh rates i get changes to these files
~/.local/share/kscreen/outputs/8c1fab27a4b0446032b782828c63118aDisplayPort-0
~/.local/share/kscreen/outputs/4f475b3b871e13934b1f517fa91da152
~/.local/share/kscreen/d56968a5243f22fc85cfa1b5a6ce2945
so perhaps backing up and restoring the entire kscreen folder will help as well