If I edit the manual curation file and change the purity and ploidy, is there any way to later on revert it back to the original PureCN-chosen solution's purity and ploidy (assuming I don't have a record of what that original purity and ploidy were)?

Would this be correct?:

> res = readRDS(sample.rds)
> which.max(sapply(res$results, function(L) L$total.log.likelihood))
[1] 2
> sampRDS$res[[2]]$purity
[1] 0.15
> sampRDS$res[[2]]$ploidy
[1] 2.925934

I think you can simply delete the CSV file and re-run PureCN.R with --rds sample.rds. It should re-create the original CSV file.