I've managed to clear my work twice now when not paying attention to where my mouse is. It's a dumb mistake on my part, but perhaps require a second click to prevent unwanted resets?

I think, if that is the specific problem, the better choice would be to:
Immediately after pressing the "Clear Level" button, temporarily change the button to "Undo Clear" until the player adds something to the board.
This would prevent the invasiveness of an unnecessary "are you sure?" window or the unintuitiveness of requiring two clicks on a button. This also has the benefit that multiple clicks on the same place will just toggle the board between the original map and the edited map; this can help someone who is trying to just quickly see what they've added so far.