configuration changes lost after activating hot fix

The configuration snapshot will be taken at the moment of installation, and any changes thereafter will not be included.

In addition to your own options, you can also roll-over the current configuration prior to switching to a new partition. This would allow you to postpone the activation of new HF. If you navigate to

Boot Location

, and modify the boot partition; at least all of the recent BigIP versions will ask you if you want to install configuration or not. That's where you should say "Yes" if the activation of HF was postponed.