When you transferred your files, just move them or rename them if possible so they will not be transferred again.
If these files may not be renamed or moved to another location, copy them from their original location to some "transfer" directory and store them there.
To save some space, you can also just write into some txt-file, which files you just transfered and filter them out to not transfer them again by checking if their names are already in the list.
There is a lot of possibilities how to do that.

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