Yes, as you guessed, the problem with a thesis Pages document with complicated footnotes, formatting and tables, was the probability of small changes occuring during the two conversions. And the time needed then to recheck the thesis with an eye for tiny things that may have changed. It's possible it could have worked, but the thesis owner decided against it in the end.
Doing it manually in Pages doesn't really seem that it should take even an hour. 
Would not you just do the 14 Replace and Seaches in Pages without using Regex?
The problem there was that the user wanted to use a different font for the flat signs rather than unicode. As far as I can see Pages couldn't do that. I had a super quick play, if you went and searched for 'Ab ' using find and then pasted the correct font 'b' over the 'b' it would take some time, again, something I would have used a macro for. Also, does 'find' go through footnotes and tables? It doesn't matter, but it's all done regardless, and in much quicker time than it would have taken me to try to work out an 'efficient' way of doing it!
Anyway, as you say, for now the horse is dead, and Elvis has left the building upon it.