Managing branched DLLs in nuget
So what is happening is that the changed code just sat until internal testing was done (never a good thing as this is how code get stale quickly).  Once internal testing was ready, the code was then merged into the trunk causing it to be published into nugget under the trunk's feed.  Some business politics ensued and we finally got to a real single code base mindset from the product owner's perspective (which was the issue that got us into this situation).  Moving forward I don't anticipate this to arise.

Code can be branched out.  However, only code in the trunk will go to our internal nugget feed or our build/deployment processes.