I got the same results as Grimoire LD. It looks like only a modified treasure list causes the glitching issue. Saving without making changes seems to be fine.

OK, I've had a chance to investigate, and I think what
should be happening is this: When adding a treasure to any given location, the way to make that treasure active is to increase byte 0C of the properties of
each subsequent location by 01 (or by an amount equal to the amount of chests you're adding). Keep byte 0C of the map you're editing the same.
For instance, the treasure index byte of Baron Town is 00, meaning when searching for treasure contents in Baron, the game starts by looking at the first treasure. But it
also references the treasure index of the
next map, Village Mist. Mist's treasure index is 07, meaning once the game has accounted for 7 treasures in Baron, it will stop counting. By changing Mist's treasure index to 08, you activate all of Baron's chests, but negate one Mist chest, because you haven't yet adjusted the treasure index of the
next map, Kaipo. Therefore, in order to add a chest seamlessly, you have to increase
all subsequent locations' treasure indices by 01 (or remove a chest somewhere).
You are right, though, that the counting resets with map 0x100 (Kokkol's smithy). I think it's safe to presume that those indices can be left alone

heh - I just re-read what I wrote... I mean they can be independent of the first set of maps, not entirely left alone.