They are likely replacing the Standard Definition channels with the HD versions first because they think it's less confusing. The customer can process in their minds easier that the HD versions are going to be the only versions available going forward. If they did everything at once some customers would wonder where their Standard Definition channels had went went and maybe assume they were elsewhere in the guide.
After all this sorting of channel numbers coming up, many of the +1 versions of channels will not be beside their main channel, many channels will be moving quite a bit up/down the guide.
Many people when confronted with too many things at once only take onboard some of it. For example, I've often found if I ask, say, 4 questions in an email to someone I usually only get 1, maybe 2, of my questions answered.
The pop-up information if they did it all at once would be more complicated, and there would be much more of it. Simple is best, but simple can mean doing things in multiple stages.