[eluser]Phil Sturgeon[/eluser]
Matchbox and HMVC both extend the Router and Loader libraries in such a way that will mean one of two things:
1.) The logic in core CodeIgniter (when eventually released) is safely over-written by Matchbox/HMVC/etc and so you can move over in your own sweet time or...
2.) There are some minor differences and you need to make a few small adjustments to your codebase. Most of which can be achieved with find/replace.
Codebase-wide changes are to be expected with a major upgrade to any system, framework, application. This case would be no different, but of course we have our fingers crossed.