I am not an SME for your situation, but I have some thoughts:
1. The situation you describe appears to be a nested/systematic component of variation study. The hierarchical layers are:
Batch (although this appears to be manipulated)
Shelf (Systematic locations, though you do not specify how many)
Samples (Confounded with the Sample component is the measurement system variation)
2. How confident are you in the measurement system? Why do you need 10 samples? You are somewhat biasing this layer.
3. Robustness is the measure of how consistent the lyophilization process is over changing noise. I would be suspicious that in 3 batches you have exposed all of the possible noise effects. You will not be able to assess the consistency of the batch-to-batch variation.
4. For analysis you may be able to use the control chart method or ANOVA method. I would start with variability plots (make sure the data types are nominal) and let JMP calculate the quantitative components.
"All models are wrong, some are useful" G.E.P. Box