I am very familiar with all of those manuals (especially Gilham's), and once again I agree with you. The only problem is that in both working for a museum and having a history degree it is drilled into your head that if you don't have the documentation you can't make a 100% claim that something happened. So while highly likely that the colors were replaced, I can't make a certain claim that they were.
Also, I remembered earlier with regard to the 47th that several years back I may have stumbled on some info that the unit may have destroyed their colors before they surrendered (they had a little more time than most units to do this since they did not surrender at Appomattox). I can't say for sure this happened until I can find all of my old files or contact some old friends that had information on the unit. If this info pops up I'll post it here.
Josh Bucchioni