I got 2 of the same file after I completed two endings (the one with Soul eater, the snake tongued-one). Is this supposed to happen?

????

idn

No, but don't delete it

Sorry, you meant you completed the same ending twice? If so, yes, you will get another file of the same.

This means you're very lucky, but if you want to use it in the OuroboroS Project you need to get a different code, that's not supposed to happen but it can, it's just rare.