Here's a screen shot of what it looks like

I've been talking to steam support (case number: HT-FPT3-WGRT-85M3) they recommended I tried running steam://resetcollections in a browser, this sadly removed about 80-90% of the games from my collections. They didn't have any further suggestions at the moment and suggested I make an issue here.
Here's a screenshot before running the command:

Here's a screenshot after running the command:

My collection "Playing sometime" went from 659 games to 69 games.
This just happened to me very recently:
The duplicates always contain a subset of the titles in the original collection.
I'm using the Steam flatpak and Steam Deck.
Nothing extracted yet.
Your system information
Please describe your issue in as much detail as possible:
Several of my collections have duplicated. This happened before on Manjaro a month back, I deleted all duplicated collections but they came back about a week later. Since then I made a fresh installation with Fedora and after a short while the collections started duplicating again. Some collections have duplicated multiple times, some hasn't duplicated at all. All of the duplicates are missing some of the games that is in the other version of the collection.
Since this might be connect to my account (maybe because I have 12,000+ games and lots of collections?), here's a link: https://steamcommunity.com/id/jpxe/
Steps for reproducing this issue: