Rewrite Protagonist... Am I the only one?

[Life]

Nope, it's a well-known plot hole that Kotarou is effectively not connected to Kotori or anything in other routes, despite that reveal in Kotori's route. Why? Further spoilers

Kotori dies in at least one of the routes, but Kotarou lives anyway. I think it was Akane route. Or maybe I'm just confusing it and that "other route death" tag on VNDB was referring to Moon.

I have a theory around this as to why it occurs.

It may not be a great theory but he rewrites himself in different ways. He rewrites himself much more in every other route as opposed to kotoris route and this could have allowed him to have a surviving body that didn't need kotori anymore. In shizurus route he was determined not to rewrite himself so kotoris connection is still a bit significant.

[Funnerific]

I have a theory around this as to why it occurs.

It may not be a great theory but he rewrites himself in different ways. He rewrites himself much more in every other route as opposed to kotoris route and this could have allowed him to have a surviving body that didn't need kotori anymore. In shizurus route he was determined not to rewrite himself so kotoris connection is still a bit significant.

Very well, but

In the end of many routes including that of Akane, his rewriting is effectively undone and he not only loses the ability, but also becomes weaker. So how? Did Kotori survive in that route?

[Life]

Very well, but

In the end of many routes including that of Akane, his rewriting is effectively undone and he not only loses the ability, but also becomes weaker. So how? Did Kotori survive in that route?

This is taking it a stretch and I can't explain it too well. The only explanation I had for that is 

Kotarous rewritten bodies heightened recovery repaired his damages before it was taken away.

Even I don't completely believe it but it was the best I could come up with.