Except they ARE listed in the rule book:
2) In the event a home team ball does not conform to specifications, or its supply is exhausted, the Referee shall secure a proper ball from the visitors and, failing that, use the best available ball.
So the first step is to "secure a proper ball from the visitors". The Colts supplied 24 balls, so there were 12 available to choose from. Why not use those? Also, "failing that" is a clause which clearly implies that the Referee is expected to make an effort to obtain visitor balls, not just leap straight into "reinflation". And even there, how does reinflation qualify as choosing the "best available ball" when the home team also has 12 unused, alternate balls available?
The whole sequence shows that even though rules do cover this situation, the NFL simply ignored them.