If I'm understanding your problem correctly, I might suggest you go in a different direction. Have you used the packrat package? Basically, it makes a library specific to your project - in this case your Shiny app. This library is independent from your usual working library, so that your app is guaranteed to run the same way, independent of anything you update for other projects.
The link below refers to Shiny Server Pro, but packrat works the same regardless of whether you use Shiny Server Pro or not.