Map Layer 2 got... weird

You can check your Tilemap ID for L2 in Zone Doctor or FF6LE and get the good pointer from here:

Code:

D9CD90     D9D1AF     Pointers to Map Formations (3 bytes each, +$D9D1B0)
D9D1B0     DDFFFF     Map Formations (350 items, compressed)

Pointer + $D9D1B0 = tilemap offset. The first two bytes of the data is your data length or you can simply take up to the next pointer. Copy this data in your ROM but make sure to not overflow on the next start of data. If you made changes to maps or maybe simply by saving with the editor, tilemaps might have been optimized so pointers might not have the exact same values in your hack.