What may be an idea in your case is to create another backup to your external drive But make sure you un-check the option to make a system image
What this will do is create a current backup of just your files and other data.
When you then restore to factory defaults (F11), you can restore from your known good backup, (system image (including all updates, programs, and settings)), and data, and then from the latest backup to restore your current data.
Once you have all your system and data to where it is before you used the F11 restore, you can create a complete back-up (data & system image ), to act as your new baseline for the future