How could qualia cause those memories to become encoded if they were epiphenomenal to brain states?

You have it the wrong way around. In epiphenomenalism, brain states cause qualia, qualia don't cause brain states.

The question was rhetorical of course... the point is that if your qualia truly are epiphenomenal, then there is no way you can remember having had them. So you're left with an extremely weak inductive argument from just one data point, basically "my brain states are creating qualia right now, so I'll infer that they always created the same qualia in the past, and that similar brain states in other people are creating similar qualia". It doesn't take extreme skepticism to suspect there is a problem with that argument.