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I’m still experiencing this issue. I’ve tried twice to validate files through Steam and both times it deleted everything in the MSFS directory. I’m now keeping a backup of the base installation on my drive. I also have MSFS2020 on the Microsoft Store, but the installation always errors out in the Xbox app after a couple percent, which made me wish to try to install via Steam. It’s quite unfortunate that both Steam and the Microsoft have their own issues that stop users such as myself from installing and enjoying the game.
I can report that Steam still does it.
Odd thing is it only happens with MSFS and not any of the other Steam games I have.
Yup, it’s an MSFS issue, not a Steam issue.
Bad user experience and system design