That should work. The waters would begin to recede after only a few days anyway, rather than remaining for months and years.
I like the idea of a flashback of him forging the Ruby Knife and the birth of Masa and Mune, perhaps instead of that smithing flashback, if only because it makes more sense and I worry a bit about creating flashbacks to stuff that mention Zeal anyway, since the idea is to avoid spoiling who Melchior is until you meet him on Mount Woe. Sure, most everyone who plays this will know who he is anyway, but it should be done to preserve the way the story is presented. (But if we can do a flashback involving the master teaching Melchior without mentioning Zeal in it, that should work.)(
That reminds me, I need to remove that reference to Melchior from Masa and Mune in Zeal Palace when I get to that point...
Oh, if we have space, can we see if we can give the Cathedral a couple small rooms to the left and right of the main chapel, just to make it look more like a real Cathedral would? Say a small library for one room, and the other to be, say, the nuns living quarters.