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Easiest method I can suggest is to Flatten (CTRL + F) and then Undo (CTRL+Z) once you're done with the plugin.

MAKE SURE YOU DON'T ACCIDENTALLY SAVE AND CLOSE WHILE FLATTENED OR YOU'LL LOSE YOUR LAYERS!

The game's been excellent so far, but I figured I should report that I found a minor mapping glitch in Legato Castle concerning the corner wall top tiles.

EDIT: It seems to happen on the opposite side too.