The Mystery of the Lost Underwear

These are the facts:

Luke went to the bathroom, fully dressed and emerged with his shirt on and his pants, socks and shoes laying on the bathroom floor.

He queried:

Mom, where are my undies? I assumed, as one might, that they must be lying on the bathroom floor near the scattered clothing that must be shed for him to accomplish what he must when he enters the bathroom for any significant amount of time. However, after much searching, they were not to be found.

The conclusion:

I'm left scratching my head because the only conclusion I can come to is that he must have flushed them down the toilet. He's very small and so are his underwear. He walked into the bathroom with them on and walked out with them missing. However, he assures me that they were not flushed. So we are left in a quandary.