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They'll be mixed in if you have them on the same device (flash, HD, cloud), but the newest ones will always be at the top. I usually just have about 10 saves on the go, so I can just delete the oldest one and create a new save each time.
Unfortunately they will be mixed, whats worse is that the auto saves will take each other over so if you are running multiple playthroughs simultaneously you will have to make sure to make a non auto save slot when you are done playing. If you don't there
is a chance that your auto save will be deleted or saved over by the auto saves from the other character. Its kind of a pain in the @@@ and I'm not sure why they decided to not split saves based on characters but it is what it is.
I have two playtrhroughs going on at the same time and the save numbers continue. ex. 1st playthrough of 270+ hours ended with save 804 - new playthrough's 1st save was 805 and the 806, etc.
I do not know if that is the same if you completely delete all previous saves, but I venture to guess that you would have to clear the Xbox cache and all traces of the game before it resets the save #'s.
Well I hope it's something they're considering patching. Seems like it would be kind of obvious that people would want more than one character without the saves being mixed up. Is using Cloud free? If so, I'll use one on HD and one on the Cloud.
Cloud is free, but what I hate is that there is a time consuming upload process each time I try to copy a save there. Not sure about playing directly from the source. Fallout Vegas was like this, with the mixed saves, it I found you had to be careful not
to overwrite something. You could always transfer your first game saves somewhere else while you play the new build, just in case. Or at least, make a copy of your most recent one to Cloud, just for safekeeping. I've done that as well.