...Right, I keep forgetting that Steam Workshop is happening.
I can't help but wonder how many of the mods I use won't make the switch, and if Itch mods and Steam Workshop play nice with each other...?
Current Itch mods and Workshop mods definitely won't work together. The Workshop update will bring a lot of changes to the base game's code that require every mod change how they do certain things.
I know a couple people that have said they aren't gonna port, but I also know someone who is willing to port those people's mods for them. I'd say it's up in the air.
You may have to wait a bit to get your full catalogue back, but I think you'll at least have most, if not all, of it back eventually.