It could be a full flood (like Noah) changing the earth due to ocean currents. Though mountains and masses with a high enough altitude would stay in tact, it would prove some of the massive changes. Ocean currents aren't as massive in power as continental drifts or even tectonic drifts. Looking at maps provided it would support my theory.
Underneath the wall of Ylisse, the upper left part, in Archanea there is a definite lower amount of land mass here, yet if you look at Ylisse itself it's nearly filled in. This could be triggered by the closing of a narrow gap, resulting in the "drying of the sea". This has happened to the Mediterranean Sea before, where the entire sea became land (which in term, resulted in the Dead Sea's high salinity). It could all be possible, but I can't say on the time period here. My example took near 40.000 years to happen. Both the start and the recovery. (fun fact, its supposed to happen again within a few centuries).
But it's still the artist and creators opinion, it isn't like they actually looked at the weather effects etc. when creating Ylisse. Or at least, that's what I think. I wouldn't be bothered by that when creating a world map :D