I just spent like 18 hours copying 600K files, 1.33 TB, from a USB 2.0 ext. drive to a 1.36 TB USB 3.0 partition, but at the very end I got a handful of prompts to replace folders that already existed in the newly created folder, asked me to merge the original folder with the one just copied on the destination drive, eventually asking for permission to replace thousands of items and that's what it's doing now. I don't know what's going on. It appears that all files are there in both folders on each drive (with the exception of half a dozen that wouldn't copy due to long filenames).
Nearest I can guess is it is writing DOS names in addition to Windows names so the computer is going to spend more than a dozen more hours doing that.
Windows Explorer copy wrongly offers to merge folders Windows Explorer copy wrongly offers to merge folders
The folder being copied that is being merged is called Drive(D), probably from a backup of Win 98SE being restored onto a Win XP machine, so it may resemble a system folder to Win 7.