I see what you want to do.
Ideally, you shouldn't have shared files that
both need modifying. You should have one repository for your shared (library) code, make the changes in that one place, then copy each changed library file to both channels' directories.
If there are minor differences between files used in one channel versus files used in the other channel, then it might be worth refactoring your code. For example, you might want to pass parameters into your utility functions so that whichever channel they are called from can pass in parameters specific to that channel.
This is more of a general software engineering issue than a Roku-specific issue, so you can really do whatever you want. My main advice though would be (a) avoid repeating code; and (b) keep things as simple as possible.
https://github.com/belltown/