After Effects Compositions Duplicating over other comps in Adobe Premiere.

Hi all,
My issue revolves around Adobe Premiere and After Effects, in particular the feature in Premiere which gives you the option to 'Replace with After Effects Composition'.
I had severail clips I wanted to do some frame painting on in my timeline, so I started with the first, used after effects, all was fine. Did the same on the second one, again, all fine, then on the third one it all went a bit wrong. After completing my frame painting on after effects, I clicked save and then closed the composition. Upon returning to Adobe Premiere and viewing my timeline the clip I had just edited was as expected, but the previous one was now a dublicate of the one I had just edited. From this point forward no matter what I did every time I tried to alter a clip in after effects it just duplicated over the other clips.
Painting frames at the best of times makes me lose the will to live, but this glitch has made it almost impossible for me to work.
Other details, I save each After Effects composition with a different file name in a different folder. I tried all sorts of different ways around it but nothing.
Does anyone know how to solve this issue, or know where I could find out. It's incredibly frustrating when you spend 10 minutes painting out dust off a video to then realise the one you did before is now overwritten on the premiere timeline.
I need help!
Louis

Before you go back and re-do your tedious retouch...
you can try opening Pr, making your Ae comps offline, exit Pr.
Go to your 'Adobe Premiere Pro Preview Files' folder, delete all.
Open Pr, relink your comps.
I've never really tried to send a series of clips to AE and edit them all as one composition, I'll give that a try.
note:
Along with sending multiple clips via DL to Ae for touchup in one comp,
When I use 'Replace with Ae Comp' in the Timeline, I will save
the newly created Ae comp, exit Ae, return to Premiere and hit 'Undo'.
This will restore the original clips to the Timeline for future reference.
Then I will use File > Adobe Dynamic Link > Import Ae Composition to
bring the new comp into Premiere, add a new layer to the Timeline
and drop in the comp (or replace the clips in a duplicate Sequence).

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