Backup of same file from two different locations The main problem here is Glacier storage class Itself.
Here's how this usually can be done with any other cloud destination:
You need to make sure the path in the cloud mirrors the one on the source by deleting/renaming the folders in the cloud and then synchronize the repository for that destination via tolls > options > repository menu in the backup software.
Since we're talking about Glacier, COPY operations are allowed due to how Glacier API operates, so the most efficient option is to start from scratch using new source location.