Changes Made to a Virtual Server Outside the iApp

This scenario does actually come up, there is a couple ways to look at it. Firstly depending on what manual changes are required you still may be able to work within the confines of the iApp. For example if you need to attach an iRule to the virtual server there is typically a section in most F5 supported iApps that allow for attaching iRules, also other things such as using an existing profile instead of creating the default, recommended profile is available through the iApp. In that case you could create the profile outside of the iApp and then change the answer in the iApp to select the profile you created.

if you cannot work within the iApp to get your modifications done there is an iApp on the codeshare that will deconstruct all the objects from the iApp and allow it to be a manual configuration from that point on. Linking to it for your further reading and use: https://devcentral.f5.com/codeshare/iapp-deconstructor