Hi @Anonymous User ,
how are you storing the feature layers in your project packages? are you adding them in by gdb, or URL, sde?
A good way to manage multiple layers, that are subject to change, is to add the layers in by using URL's, if you don't have one you can share layers in portal, and reference the layers back from portal into your project package.
This also ensures that edits made to the features/ feature services are reflected back into all the products ( ie the project packages)
let me know about how you add in the layers, and I would be happy to help