Ok so I stupidly did the safemode database rebuilding without a backup and sure enough all 40 of the games on my PS4's 2TB HDD disappeared, at least according to the XMB. FTP'ing into the console showed me that they were still there however. So I ran Stooged's PKG BACKUP payload and it transferred all of the packages to an external HDD. I was initially very unhappy thinking that I had well and truly borked my system but thankfully said payload saved my proverbial bacon. The more you know!