If you play through a level, then press the replay hotkey, the minimap itself does not reset. See pictures below.
However, after pressing the replay hotkey, then when assigning a skill to a lemming, the minimap will then reset to normal state.
This isn't worth releasing a V1.43n-G update for, but as it's (probably) quite a simple fix, if one becomes nessecary anyway I'll slip this in. Otherwise, I'll do the fix in the next major update, whenever that comes (it may be a while).
Fixed for next update.