So they deleted skyfall estate I guess, but I had a ton of stuff in there, is it all gone?

What do you mean? Deleted from where? Here's a http://www.nexusmods.com/skyrim/mods/50480/? and http://www.nexusmods.com/skyrimspecialedition/mods/2185/?.

But that wont help me on the ps4 right?

So it's like, gone on the mod list, but I can still see it in the load order section, so I think I'm just going to clean it out and take the mod of I guess

which I'm kinda sad about tbh. I really love this house.

if I take all the soul gems out, will they still be in my inventory when I disable it?

If you like the mod, why would you disable it?

If you already have it, it stays. Because it's removed from the download list doeN't mean it deletes yours.