Hi Jason,
Are you able to see this TechNote on SupportNet?
How to instantiate a list of GDS files into a new composite GDS file
It shows a way to use a Tcl script ith DESIGNrev to merge GDS files together and account for clashing of same cell names.
Here's another TechNote showing how to rename cells with a script.
DESIGNrev Tcl Script to Rename Cells
Maybe both techniques could be combined to accomplish what you want?