I want to propose two more possible solutions.
First, as I initially assumed, wards that Quirrel cast at Mary's are rendering them undetectable to patronus communication. That way, if there were no second Harry in Azkaban and third Harry on the way back, McGonagall's patronus wouldn't be able to contact him at all.
Second, for all we know about patronus' methods of travel, it might get autonomously dispatched directly to target's location, which is normally unique. There are no conservation laws that prohibit patronus splitting into two independent messengers, as there are no conservation laws preventing you from having two mirror reflections, or two acoustic echoes at the same time; and reflections and echoes can be interacted with in magical ways in Potterverse. That means that all two or three copies of Harry can get the same message, give non-conflicting answers, and McGonagall won't suspect anything.
- This thread has run its course. You will find newer threads in the discussion section.
Another discussion thread - the fourth - has reached the (arbitrary?) 500 comments threshold, so it's time for a new thread for Eliezer Yudkowsky's widely-praised Harry Potter fanfic.
Most of the paratext and fan-made resources are listed on Mr. LessWrong's author page. There is also AdeleneDawner's collection of most of the previously-published Author's Notes.
Older threads: one, two, three, four. By tag.
Newer threads are in the Discussion section, starting from Part 6.
Spoiler policy as suggested by Unnamed and approved by Eliezer, me, and at least three other upmodders:
It would also be quite sensible and welcome to continue the practice of declaring at the top of your post which chapters you are about to discuss, especially for newly-published ones, so that people who haven't yet seen them can stop reading in time.