Are they really identical? Is the origin in the same location for all?
If so, select all of them in the assembly (use advance selection to do it fast) and replace the components files with one file. There are no mates in the imported assembly, so it should be fast (no questions asked).
OK, I just took a few minutes and looked at random multiple files.
And like you said, Alin, some weren't exactly the same but others were.
Some ended up being multi-body parts like the same washer body in a pattern of 6.
But like I said, some were the exact same. I overlayed them using their origins in a dummy assembly and they matched perfectly.
So in light of this new information, I wouldn't want to blindly replace components in the main assembly.
So I guess I'll just leave things alone. It would be too time consuming to sort that many multiples out.
That would be a good time to use configurations with those -2, -3 type parts