Was my client [name withheld] waking up to a sewer smell that persists due to her visiting a waste disposal plant and its reawakening a past life trauma of hiding in a sewer with her family to escape death from pursuers?

This is, in fact, the case. As you saw during your Protocol session on her behalf, this was the trigger of the emotional reaction and the knowledge of what came before and the proximity of the same players. So this is causing emotional turmoil within and she is being warned of this through the olfactory senses, re-visiting the prior scene of the crime, so to speak.