If I've run PureCN once and generated output files including .rds file, if I run it again and specify the --rds argument and give it the name of the .rds file it created in the first run, (and otherwise give it all the same arguments as in the first run), will it re-create all of the output files it created the first time?

Yes, if you run it with --rds, it will open the CSV file, pick the solution closest to the there specified purity/ploidy combination and re-create all PureCN.R output files (instead of the default of creating the output for the maximum likelihood solution).