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It sounds like you have some code files that might get changed along with all the other code files, but these particular code files also change -- from your end -- for the branding process.
If possible, it would be wise to move all brand-related items/strings/graphic-paths out of your files and into their own subset of new files, or even a database (similar to the process of abstracting strings for localization purposes). I realize that developer effort may be required to do this. For example, if one of your code files has a path string that points to a graphic, and the string changes depending on the client, instead make the string always point to one resource that the developer never messes with and which you swap as you see fit.
The goal would be to entirely separate the code (which the developers can change) from the branding (which you are apparently in charge of). Then the developers can change code all they want, and the only thing you need to keep on top of is new, brand-able resources and making sure that the correct brand is included every time you put together a release.