I done the same thing when this all started. I could only select slot 3 when the glitch appeared, so I copied my playthrough from slot 1 to slot 3, and I tried a couple of times before the patch to play the copied slot 3 game but the decisions were not mine.
When I finally got the patch today, I tried testing it on the back-up slot 3, my decisions were all messed up. I was thinking the game was still broken. but then I tried my original slot 1 save (out of desperation), it worked my decisions were still there for the most part (episode 1 stats were gone, but 2 & 3 were intact - and my story was unaffected) I've just played through Ep.4 without any new problems.
This may not work for you, but you may as well try it at this stage, if you've already downloaded the patch: just load your original game, look at the stats and if they were your decisions, just play. As far as I can tell, before the patch was released, copying your file, corrupted your stats on the new slot, but didn't ruin your original save.
I was still asked to random generate choices for unplayed episodes, but it made no difference to my game.
I hope this helps, but if not please don't track me down and murder me.