@ tracy – see the steps to restore all plugin files in this link below that goes to a previous post in this topic.
http://forum.ait-pro.com/forums/topic/plugins-have-disappeared-after-updating/page/2/#post-15671
We just completed new code in BPS Pro 9.0 that will take care of this issue permanently. Testing is completed and a new BPS Pro 9.0 zip file will be uploaded shortly. I will post more details in a follow-up post about what this new code does and what potential problems it prevents from happening using a FailSafe shutdown for the ARQ Cron for various conditions that are most likely causing this issue/problem, etc.
Just an FYI – the reason you cannot restore all files at once from Quarantine is due to limitations imposed by your Server. That is why we created the Sort/Search feature in Quarantine. On our dedicated testing server we can restore 1,000′s of files at the same time without a problem since we set the limitation ourselves on our Server. On our Live Shared Hosting server we are limited to restoring about 400 files at one time max.