DFF / Replace vs. Entire New File

[user1679]

Question:

If I create a patch that replaces an entire file instead of using DIFF to replace cues, will I end up with duplicate cue instances?

Details:

If I have a file: myfile.xml that has a bunch of cues in it that I might want to do something else if there is another mod installed, is It OK to create a patch mod that simply has a different version of myfile.xml instead of doing a DIFF/Replace for every cue? The new file will still have the same CUE / CUES defined, they will just have different actions within each.

Of course I'd control the loading of the patch mod using dependencies.