Hi,
as @hobanagerik mentioned, after choose the “Steam verify” you have to reinstall the whole game content (if you not special backup it). Does it happen in your case or is the only download you see these 53MB ? If you not have to redownload the whole content, it sounds like the game content was not wiped and may be it’s the same reason why the “update” is not realy done and your CRJ goes away.
I remember some topics about these issue with " missing packages ".. so far I remember it points to corrupts files.
As example in this topic are mentioned some file tweaks:
May be a full re-install can fix it… Important is then a uninstall as in FAQ described: https://flightsimulator.zendesk.com/hc/en-us/articles/360016125019-Steam-How-to-repair-remove-and-do-a-clean-install-of-Microsoft-Flight-Simulator ( check and delete folders which possible not removed from uninstaller ).
I hope it is not caused by a invalid “config setting”, because the MS users mention the /wgs" folder. If so, you can may be try to clean Steam cache.