The development that losing their powers should have brought wasn't just them coming to understand that they're special to each other. It was also coming to terms with themselves. The reason they started swapping was because, back in chapter 1, they envied and wanted to be each other. That's the "desire", and that's also why the NTR swap happened in chapters 49-50. Losing that desire means coming to value their own selves. It means they're happy with who they are, and that if they still consider each other special, it's as a companion rather than an object of envy.
Giving them back the ability to swap completely undermines that.
Of course, I dislike that explanation anyway, because of what it says about the other couples (especially the long-lasting sensei pair).