RTF is a global modification that replaces all towns in the game.

How did the rebalancing of the Conflux affect the Phoenixes?

I didn't touch the last two levels because they will be replaced later, and therefore I decided not to bother with them (since the abilities will be changed and the stats too).
And specifically regarding the Phoenixes - IMHO, it's better not to touch them; making them weaker is not an option, and removing the resurrection ability seems strange.