I use pack and go as a way to clean out a folder of the parts that aren't used anymore. I was going to rename a part as well, but noticed in the nested view the part was listed multiple times if it was used more than once so I'm guessing that isn't the place to rename files. I noticed the nested vs flat and didn't understand what the difference was. Does that make it only show one instance of every file? Could I use the flat view and then rename files while doing the pack and go?
I think it is only a visual aid to see where the parts are used etc... I use the flat at times to check the "Short List" or rather summarized list of all the components..
I use the Select & Replace to rename the components.. Also Pack & Go in a different folder, I go C:\User\.. \Documents and save my PG there..