We've found that sometimes the Steam client won't properly update or uninstall Workshop items for some users. If you run into Workshop trouble, here's some workarounds that might help.

Steam Cloud is required for Workshop to function, so make sure yours didn't get disabled somehow. There's two places to verify this:

1) Steam -> Settings -> Cloud
2) Select Star Control: Origins from your Library list; right-click and select Properties. Check that you have Cloud enabled for the game.

If you find Workshop items not updating properly, try the following:

1) Favorite your Item so it's easy to find again and unsubscribe
2) Exit Steam
3) Open Explorer to where you have Steam installed: Steam\steamapps\workshop
4) Open appworkshop_271260.acf in Notepad
5) Remove all the entries under WorkshopItemsInstalled and WorkshipItemDetails within the { } sections.

For instance, you should have:

"WorkshopItemsInstalled"
{

}
"WorkshopItemDetails"
{

}
6) Save the file and exit notepad.
7) Start Steam and subscribe to the items you want.