I tried cleaning mods and reinstalling them as you have said. However this problem is not related to any mod. All the mods that I have installed together or separately is working but after a restart I get same warning. Like you have said I tried deleting other files than savegame and I found that deleting only mod file and launcher-v2.sqlite solving problem. And lastly I found that after restarting pc, paradox launcher itself is also cannot be found too so it also needs a clean reinstallation every time that I restart my computer. At this point I think we can clearly say problem is the launcher itself. For me it is not a problem to reinstall launcher and delete necessary files for them to be recreated by game however this is obviously not a real solution it is only a workaround. I hope this will be solved in future releases of paradox launcher.