Why is this problematic?
Because the steam client is reaching somewhere it isn't wanted. If a user removed a game via steam and installed it via something else, there's a reason. If they still want steam to be aware of it, they can easily add it back via the add a non steam game option, but as far as I can see there's no way to force it to forget a game in this manner, even though it's implied by uninstalling.
Nothing extracted yet.
Your system information
Please describe your issue in as much detail as possible:
I own certain games on both itch.io and steam. For some reason, some of these show up in the steam client even if I installed and manage them through itch. I'm not sure if this is related to steam cloud or not, but so far every game I've tried it with has had steam cloud.
In each case so far, I've had the game installed in steam, then got it through itch for whatever reason, and removed my downloaded version in steam in favour of the itch version. It no longer shows up in my installed games in steam until I launch it through itch. At that point, it remains visible in my steam library (complaining about the steam cloud sync) until I quit and relaunch steam.
Steps for reproducing this issue: