I used to host custom map, server was online for 2 days then next morning auto restart happened and map structures were gone. I though it's a custom map issue, so changed to procgen map... It was ok but when next morning auto restart happened server just again autowiped, map got corrupted or idk. No player bags, building or etc are on the map. Any ideas what it could be and how to fix the issue?

Take a look at your auto restart script and see what it is actually doing.

My Pterodactyl panel has scheduled tasks. I do set power action to restart, and worked fine for around 1 year and it does it properly. Not sure what the issue is, just bought a plugin "XRestarts", which do not start the server (only stop it) but somehow without any setup from my side it auto starts. And last day everything seems fine with my map. It was weird issue but it's OK now. Still not sure how to see what corrupts in these scenarios if happens again.

Make sure your server is saving properly. If everything wipes upon the server restarting, it would indicate that it is not saving properly. Make sure all of your plugins are up to date, make sure your server steam / umod are up to date. Once you do that type save in the F1 console and monitor your RCON to see if the server saves backpacks/banks/server entities and such. If you do not see it saving, then you will need to identify the cause of that issue and once resolved it should resolve your wiping problem.