If you have the need to manually change the configuration outside the iApp, there are at least 3 ways to protect yourself. One way is to prevent subsequent reconfiguration by changing the Template field in your iApp to "None - Do not use a template". Henceforth, nobody will be able to modify the iApp, and therefore nobody will overwrite your manual configurations. A second, more radical option is to completely disassociate your config from the iApp using the iApp Deconstructor (see https://devcentral.f5.com/s/articles/iapp-deconstructor). The Deconstructor is not fully tested or supported as of March 2016, and is only for advanced users. The down side to both of these options is that you can no longer use the iApp to manage your config. If you wish to safely manage your config with the iApp, have outside changes to make, and do not wish to customize any iApp code, you must build an internal process whereby you keep a list of changes made outside the iApp and re-apply them after each time the iApp is reconfigured. You may learn by iteration that some changes need not be applied each time, but as I explained in the article, there is no easy way to know without checking.