Actually whatever caused the ARQ FailSafes not to kick in to prevent the BuddyPress plugin files and other plugin files from being quarantined is really to blame. There is a critical timed sequence of events that must happen without any interruption and in perfect sequence. A server hiccup or lost connectivity for only a millisecond is all it takes for this problem to occur. Then the other factor is that if you have a plugin or theme that has dependent files that must be where they are supposed to be and they are not there then you will see a blank/white website. Luckily this problem only happens very rarely and there are very few plugins and themes (around 5 total) that have dependent files where this problem can even occur. It is fairly easy to fix this problem. Just requires manually copying files.
Nope, BPS Pro should not be updated manually. That can actually cause this problem due to the critical timed sequence of events not happening when they should. There is one particular file that contains all of the ARQ filters and if that file is missing/not yet installed when the next ARQ Cron fires then that is when this problem occurs. A typical WordPress plugin update/upgrade deletes all of a plugin’s files and then adds new plugin files. So actually there is a 100% safe BPS Pro upgrade method where it would be impossible for this problem to happen – if you use the BPS Pro Upload Zip Installer it overwrites/replaces BPS Pro plugin files instead of a deleting old plugin files and then adding new plugin files like the WP Upload zip installer or the WP API plugin and theme upgrader.