Is the 29 gallon possibly a BioCube? If it is the original model, they could have jumped into the back chambers... Happened to me a lot with saltwater.
If you're 100% sure your tank is flawless, perhaps they're getting sick and dying in the plants for some reason, in places you can't find them. Maybe they're getting stuck somewhere, like under driftwood or rock.
Is it possible any of them went nemo-style and swam into the filter, but unlike nemo, failed and got sucked in?
Do you have anything other than fish in the tank? If you have a REALLY good cleanup crew or shrimp or something, it's possible that the fish could be dying from something (illness, injury) and swimming into the plants to die, then they're cleaned up before you can find them.
I had this happen to my first clownfish when I had saltwater. Tore the entire tank apart -- took out every rock, looked in the filter chambers, everything. Never found.
Is there any way something could have gotten spilled in the water to contaminate it? Maybe heavy metals or something? Broken thermometer, heater, ect?