If you have a backup of the original non-working perl64 folder, you could compare it with the working perl64 folder using a program that can compare folders, like WinDiff, or WinMerge.
Then you'd copy different files files that are different or missing, one at a time from the working to the non-working folders until you'd fixed it.

After that you should delete the "fixed" (previously non-working, but now working) perl64 folder as some modules would be in a half-installed mess. Then do a proper install of perl64 and apply the info you learnt when you fixed it.


UPDATE: corrected ambiguity in my English:
s/different files/files that are different or missing/