So, how many Fire Emblem projects have been financed because of this?
Generally how these types of things work is less "We take money from Game A and put it in Game B," and more that IntSys will be given whatever budget and partners they want to work with based on their strong success.
Similarly Nintendo will be more willing to let them experiment with whatever they want to try. Fire Emblem Heroes doesn't improve the odds of an Advance Wars game by virtue of the money it's making getting pumped into Advance Wars, but by raising IntSys' corporate stature significantly to the point where their publishing partner really wants to keep them happy.
The reverse is also true of course. When they were making Awakening, they were told they had to sell at least 180,000 copies or the series would be kaput, and presumably they would have to go work on whatever Nintendo wanted them to if they wanted to keep working with Nintendo. Of course, given they beat that number by more than 10 times, the balance of decision making here completely flipped.
Fire Emblem Heroes was also IntSys's idea, from concept to monetization structure, and they pitched the idea to Nintendo after they heard Nintendo was interested in making mobile games, so they're assuredly viewed very, very positively right now.