Cannot create new selection groups after mistakenly recording with Group Clips In Folders

Okay... this is a problem. After being away from my project and the DAW for a while I went on a flurry of tracking. However I had previously set the Recording options to Group Clips In Folders and I had rearranged the folder structure of the project. Kind of hard to explain... so I'll just explain what's happening.
 
I have two guitar tracks that are essentially multi mic'd versions of the same source (two line outs from my amp recorded simultaneously). ALL of the takes have been automatically put into the same Clip Selection Group. What I wanted (and what I managed to get before) was that for each take I did ONLY that take got grouped with the corresponding take in the other track. 
 
So each take I did was assigned to one selection group. Then if I edited one take in one track the corresponding take in the other track would follow those edits. All the other takes in both tracks had their own selection group.
 
This time though what happened was ALL the takes I did got assigned to the same group. So every take in both tracks are now in selection group 115. If I select one take it selects them all. If I try to speed comp it goes all weird and I can't comp properly.
 
This is my fault because I screwed up and recorded with everything in a folder.
 
Now though when I remove all the takes from selection group 115 and try to create new groups for each set of tracks they REFUSE to create new selection groups. So I...
 
a) Remove all the takes in selection group 115
b) Select take 1 from the first track and take 1 from the second track
c) Create a new selection group
 
This creates selection group 115 and places both those takes into that group which is fine.
 
When I move on to the next set of takes though instead of creating selection group 116 and placing those takes into it what happens is it assigns them to group 115 again.
 
Basically no matter what I do I cannot make these clips go into a new selection group. They always go into group 115 which was the original group they were recorded into.
 
How can I force these clips into their own selection groups?
 
Sorry if that's crazy/confusing but it's really weird and is causing me some major issues. I know I must be doing something wrong.
 
Cheers and thanks.
 
Edit: After removing all the takes from the selection group comping is working properly again across both tracks. I have no idea what the heck is going on with this but at least I can work. I'd still like to know how to fix the selection group weirdness if anyone has any ideas.