Visual Novels and Replays

So, I've only played 3 proper visual novels from start to finish. Whereas CLANNAD had a "true" ending which can be considered "beating the game" proper, and Tomoyo After only had one real ending, the VN I'm currently playing, Kanon, is different.

Kanon is one of those VNs with different paths and no canon or true ending, so beating each route is considered beating the game, however, only one part of the entire game is shared between all routes, and then each route has its own length, which means that if I beat the game with Makoto's route, it's really not gonna be the same as beating the game for a second time doing Ayu's.

Given this, how should one approach marking these playthroughs as a "Replay"?

I wouldn’t mark these as replays and suggest the following for all VN’s.

Main story - Your first route
Main + extras - Your first route and any additional routes and your current progress (detail how many routes in the notes)
Completionist - all routes

It’s up to you if you record a single time that you move between categories or record each category on the same “playthrough”. On some games the first makes more sense due to non-linear routing (say, Virtues Last Reward), on other games you might as well do all three.

If you do end up making different submissions for each route, be sure to mention which route the time is for in the completion notes.