You can have one animation “idle” for Skeleton A and a different animation “idle” (with the exact same name) for Skeleton B as long as they’re in different directories in the Content Browser and, subsequently, the Project Folder.
In order to be able to modify the retargeted animation (in this example, “idle”) from the DCC, on the fly, with UE4 open, designate the import source in the details panel of the anim asset.
Here is an illustration of the result:
At this point we have a modified “idle” animation for Skeleton B so that this specific/modified animation will be called for Skeleton B (in the State Machine, etc.) while maintaining the original “idle” animation for the original Skeleton A.