Deleting the .patch folder really shouldn't do anything, as the launcher (when working) would create a new one if missing. Keep the renamed folder around, and when we fix the launcher problem and you have patching issues you can copy the contents over to the .patch folder.
I really don't understand where does this problem come from. It affects people at random, at best, or maybe touching only Oceanics? Does Cryptic have 2 server blocks that they take down in succession before patch night?