How do I stop Macbook file duplicating 01. duplicating.02?

I think my question heading explains it.

I made alias files for my logic pro x folders, I have recently updated logic and the alias' have been removed. I then went into the original files on my external HDD, copied the contents of folders to the the new same named folder (thinking it would ask me if I wanted to skip any files with the same name) and now I have a bunch of files that are duplicated.01 duplicated.02 just like that so any duplicate delete apps will not pick up on it, ok, breath and full stop.

Is there a setting to stop this from happening?