Thanks ICade
I did actually try shift dragging but the new version was also locked on phantom.
I ended up on LiveChat to Linden who sent an agent over to have a look and we then discussed it for a while.
In the end, the conclusion was, this is a bug, and they weren't able to help me further with this issue.
I submitted a bug report and was feeling rather sorry for myself.
BUT...
I'm very pleased to say I've found a solution so obviously wanted to share it here for anyone else who has this issue.
If you build a new object (anything will do, so the default wooden cube is fine) and then link the broken phantom prims to the new object, and then finally unlink them, the phantom prims go back to normal!
Very pleased indeed to have solved this one as I really thought I'd have to start again on my build which would have been awful.
If anyone finds themselves in the same situation and the above is not clear, hit me up in world and I'll help you out.
Thanks so much to those who posted in here to help.