If I change the filename for a rom, then I would have to manually edit the gamelist.xml (and cache/<platform>/quickid.xml) to keep the mappings intact?
You can do that if you are interested in keeping any details in the gamelist.xml such as play count in tact.
Skyscraper should just add a new lines for the new names in the quickid.xml and the old names would just become irrelevant. I recently transferred the quickid.xml files from one system to another along with the cache folder to avoid having to re-scrape my roms. Then I realized I had some different rom files on the second system and Skyscraper just made extra lines for the files it didn't recognize and didn't try to scrape the ones that didn't exist anymore.