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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
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126GB to be re-downloaded without any need / warning. That’s just… annoying… 
This is a current limitation of our custom install setup according to the devs, with nothing that they are able to change at this time. We will convert this to a Wishlist item as it is a task for future development.
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Thank you for the feedback. Really hoping they revisit this for the next iteration of the sim.
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It’s because Steam doesn’t host the files, Microsoft does.
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Ugh. A warning that 130GB of downloaded Official Packages would be wiped would be nice.This just happened to me as well after I had a crash to desktop. Tried verifying the files through Steam, and it deleted all 130GB of files located within the Official packages folder! Fortunately I’ve got a backup of the content, trying to copy it back over right now. Got my fingers crossed that it works.
Steam doesn’t host the files as I posted above. That’s why no warning. As far as Steam knows, it’s just 2 GB or w/e.