When upgrading WordPress, BPS Pro handles everything automatically. When you are manually upgrading Themes or Plugins then an additional click is required on your part. Theme and Plugin updates cannot be automated in the same way that WordPress upgrades are automated. I will not bore you with the numerous technical and logical reasons for why that is. I believe in this particular scenario you probably could have just done these steps:
1. Turn Off AutoRestore (when you cannot log into your site see AutoRestore/Quarantine Troubleshooting & Problem Recovery below).
2. Upload just the Themes folder.
3. Go to AutoRestore and click the wp-content Backup Files button to backup your new Theme files.
4. Go to Quarantine and delete all Theme files that were quarantined.
AutoRestore/Quarantine Automation Help Reference
http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/#automation
AutoRestore/Quarantine Troubleshooting & Problem Recovery
http://forum.ait-pro.com/forums/topic/autorestore-quarantine-guide-read-me-first/#ARQ-Troubleshooting
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