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I have noticed that there are many people that don't really get the save slots on Borderlands 2, such as when they are resigning or trying to use a save slot of something like 1339
If you don't know what a save slot is/number of your save slot it can be found at the end of your save being 4-digits long! Example: BLUS30982-SAVE-SAVE0001 (The 0001 is your save slot/slot number)

How Do I Resign My BL2 Game save if my slot is 0001 and the modded save's slot is 1339?
Now to what people really want to know is how to resign a save slot that is higher then there's or not the same number as there save slot number. Its actually really simple as you don't have to have the same slot number as the modded save! All you must have is any kind of save that's from your profile as it could even be a save from a different game, but you just need a save that's been created from your profile so you can use it to resign the modded save. Now that you have a save from your profile and the modded save you want resigned all you have to do is simply resign it like normal with Xploder and once you have done that you should now have 2 saves on your USB drive unlike normally you would only have 1 save after you had resigned it. And now just copy it to your PS3 and your done!

Note: Using a save lower than your current Save will end up overwriting your original save! Example: my save BLUS30982-SAVE-SAVE0006 modded save BLUS30982-SAVE-SAVE0003 it will overwrite you current 0003 save! Just a heads up

I agree with you but with an exception of different result. I managed to duplicate two files, rename the save folder (internally) using SFO editor and the folder name.. using SFO editor and later resigned it with Exploder. It seems to work, it doesn't overwrite my save file but I cannot load two save files at the same time as two different characters It means, that PS3 cannot tell the difference that they are two different characters even after the renamed/resigned.

It's probably both save files' names remained the same. There is two different SFO editor. I also using the SFO editor from aldostools.org (from PS3 Tools).