It sounds like you are attempting to sign your .app bundle, upload it to a web-server, and them modify a .plist value inside the .app wrapper before the .app bundle is downloaded and given to a customer.
Gatekeeper will not allow this. (At least, it will not allow it with "version 2" signatures, which are required for deployment on OS X 10.9.5 or later. It was permitted with the older signing system, so if you are content to deploy on OS X < 10.9.5, you could get away with it.)
See Apple Tech Note 2206 for reference (in particular the FAQ "I want to exclude files so I can fix my bundle after I build it"):
https://developer.apple.com/library/mac/technotes/tn2206/_index.html#//apple_ref/doc/uid/DTS40007919-CH1-TNTAG302
Note: If you modify your .plist entry as you say you will end up with a broken signature, but all hope is not lost. If your users have the default security settings, they can still right-click on your .app bundle and say 'Open.' This will result in some scary security warnings from Apple, but if your users persist in clicking 'OK' then they will be able to run your app just fine.