I usually see mine. He's always on my rocks or on the glass. The other one either got sucked into the overflow, or he crawled there. I can easily find him. Which reminds me, I should move him out to the main part of the tank.
What type of nudibranch do you have? Most all nudibranchs die of starvation unfortunately, and do not do well in the high flow/overflow environment of a tank.