My thoughts:
What you do depends on how the actual data was gathered. It is possible you have multiple components confounded in the measurements:
1. Part-to-part,
2. Within part, and
3. Measurement
I would first look graphically at the within treatment and possibly assess the consistency within treatment. Then, as suggested calculate appropriate enumerative statistics to summarize the within treatment data (mean and variance) and then model both response variables.
"All models are wrong, some are useful" G.E.P. Box