Regression on old super-flat world's chunks conversion

I did not test if previous versions are affected, but 18w49a and 18w50a does affected.
I'm using an 1.5-era map downloaded from here, it works pretty well in 1.7.10, 1.8.9, 1.12.2, but in 1.13.2 the potions in chests won't be upgraded and portal blocks are missing.
It uses a customized super-flat setting instead of the default one, so in 1.13.2 it seems to be pretty fine as 1_13_2.png.
But in snapshot versions, those chunks are regenerated and overwrite the blocks.
I also tested the well known map World of Worlds, it's an 1.10.2 map, this problem also occurred.