Sorry but I have no idea about the current state of your deployment. From what you are saying you use some strange deployment approach that makes no sense to me. Possibly you have some mismatched versions between features and core but I have no way to help you.
I do this for all the modules and changes I work with
It sounds like you forked the code and painted yourself into a corner that makes it hard for you to upgrade without breaking things.
Deployment packages I produce all work correctly.
It does not sound like you understand correctly how to publish from source code and make your own deployment package. You should either use deployment packages I produce or complete packages that you produce but you should not mix files between those choices and especially not between your forked versions of features and my official packages.
To learn how to correctly publish see Packaging and Deployment.
See also Avoid Forking the Code.
Hope it helps,