I'm going to assume that just as the Cyclops lifts his left leg Lourie will manage to carve out his right with her shovel, causing it to fall over into the water. It's called the Shovel of Aggression, so I can only assume that allows the user the ability to shovel very aggressively to the point where they could literally take chunks out of other creatures by way of using the skill. It's either that, or Lourie will bring the rock back into storage, causing both the Cyclops and Tsuguto to fall into the water. While Tsugoto will have a hard time swimming with a broken arm, he'll be able to use his Evil Eye without issue. So can the Cyclops, I suppose, but the Cyclops' pressure will mostly affect the water, and that lake is a lot deeper than the little puddle it was playing in earlier. Far too much water to displace it all enough to cause Tsuguto to kneel again.
@Owyn Iirc, Lourie said the dungeon restoration happens sometime around midnight each night. They initially decided they needed to kill the Cyclops about 24 hours before they actually went through with the plan. If we assume the entire fight from when Tsuguto aggroed it to when they lured it to the pitfall took about 30 minutes then it's likely that they started initially discussing the plan for a while right before the previous midnight (let's say half an hour before), started moving the rocks right after the previous night's restoration, and by the time they were ready to fight the Cyclops it was already nearing midnight of the next night and thus the next dungeon restoration. The timing was just really bad.
@BananowyJE I assumed the same about the walls, but I guess we were wrong.