be happy, in Steam is much easier to do that , and much less issues with Steam installs in general.
Cleanup of ALL cloud files is easy:
Tricky will be if you not want to remove all files.
You can as example backup all your steam-cloud-files (Playtime gone missing [Packages out of date] - #31 by MichaMMA) .
Manually from these steam website: https://store.steampowered.com/account/remotestorage
or per backup the local cache folder :
C:\Program Files (x86)\Steam\userdata\xxx_your_steam_id_xxxx\1250410
( note: 1250410 stands for MSFS app-id )
In this way, you can later also stepwise restore files. E.g. for some users the logook file becomes corrupt, but not the input_ files ( joystick settings ). So you can later restore e.g. the joystick settings and only loose the logbook.
What you need to do for testing is then , after the backup of the files, to disable in Steam the Cloud-Save for the Game. Then remove the local cache folder for MSFS. In best, just to be sure, clean app also the folder %AppData%\Microsoft Flight Simulator. Simple remove all files/folder except ! the Packages folder ( if you have the packages installed in default, these folder contains all of the content ! ). Result is a clean start of MSFS.
If that works you can decide to enable Steam-cloud again and use the “clean start”-data. Or you can do future tests with the old data. In each case Steam ask you which files should be used when you then re-enable the cloud-sync again.