No they will not be removed from the mixed folder.
What you could do is as follows:
1 - Pack&Go to a new folder
2 - Copy all the files (obtained from Pack&Go) back to the original folder (overwrite the existing ones)
3 - Sort by "Date modified" in Window Explorer
4 - Delete all the latest files (Date and Time of "Copy" operation)
I know it could be dangerous. Just double check the numbers of files to be deleted matches the number of files in Pack&Go.
Hope it helps.