I had 2 folders of a mod with the same name, one had an apostrophe in the name (which turned out to be the reason the server wouldn't run the mod) I had to take down the mod from Workshop and remove the apostrophe from the name and then republished it. I then subscribed to the new mod but when I looked in the !Workshop folder there were the 2 folders still there.

This is where I think my bigger problem occurred, I deleted the mod folder of the old version as Steam had not done so even though I'd unsubscribed. My question is now does Steam still see the original mod folder when loading the launcher? I am being kicked from my own server as it says I have a pbo from the old version and the launcher show 2 versions upon launching, on one side the old mod name and on the right hand side the new version. Thing is all the pbos are the same anyway.