A very good way to deal with that problem would be to store the
comments outside the game, like Rybka Aquarium

"
Chess players who are mostly used to working with game notation, comments and
variations are in for a bit of shock when they realize how much Rybka Aquarium
relies on chess trees and the new opportunities offered by that approach. Chess
trees can be created for the opening, middlegame or the endgame. You can even
create a chess tree for a whole database including every move in every game.
Aquarium can also include game commentary in trees, which makes them much
more useful for studying openings. Aquarium also uses trees for storing and
displaying the results of engine analysis, from simple infinite analysis to the
advanced IDeA analysis method.

The advantage of storing analysis and commentary in a tree is that it
is accessible
in any game where the same position occurs. Aquarium will not be fooled by
transpositions: Regardless of the move order used to reach a position
you will see
all the data that is available for it.
evaluation tree.

"

Source : http://chessok.com/files/Aquarium2010.pdf

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