You can try editing the xml files in the LCM directory and import them, but can't you rename the folders after importing them (I don't how IR works, but wouldn't that be an easier approach)?
Thanks for the response Celvin.
My current dev environment was an import of prod (done prior to my arrival). So my root folder structure is almost identical. However, these reports have been modified and replaced in between then and now. I want to keep these folders/files intact so that the developers can continue working on them and not be affected by my work. My goal is to import the complete folder structure with files from Prod into a separate folder in Dev under root. When I import now from Prod it just overwrites my current folder in Dev. If I could just import and rename I would rather that than messing with the xml but I don't think that is an option in my situation.