Here are my thoughts:
1. Do you have any idea from past experience or previous data collection how much the batch-to-batch variation there is? Is it consistent? Can you represent the future variation in the batches in just a couple of batches during your experiment?
2. Do you have any hypotheses as to why there is/may be batch-to-batch variation? Are you interested in studying this?
3. Here are some answers to your questions:
Blocking is a strategy to handle noise. You do NOT want to confound design factors with the block. The strategy is to keep the noise "constant" within the block thereby increasing the precision and then purposely varying THAT noise between blocks to increase the inference space. If you can assign what factors are confounded with the block (that is you know what those factors are), then it seems reasonable to treat the block as a fixed effect and then be able to estimate the block effect and all block-by-design factor interactions. The later are extremely useful for robust design. If you want to be robust to noise (in this case supplier material batches), then determining if your design factors have a consistent effect over changing noise is critical (this is estimated by the block-by-factor interactions). If you cannot assign the noise, then likely you treat the block as a random effect and you will not be able to estimate noise-by-factor interactions. As is always the case, the more you understand about effects such as Batch or Day, the better your options.
Can you control the batch effect? I think not. This by definition is noise (a factor you are unwilling or unable to manage).
4. As I see it you have the following options:
- Use sampling to understand the batch-to-batch component of variation. This would be quite useful in determining the strategy to handle this in an experiment. I would add this strategy to understand Day variation as well.
- Confound the batch with the block and treat as a random effect. This will increase the precision of the design and increase the inference space, but will not allow estimation of the robustness of your process to batch variation. There is still the question of how representative are the batches in your experiment of future batch variations (thus randomly select batches)
- Confound the batch with the block and treat as a fixed effect (this is Box's quote you have included in your post "Block what you can..." means what you can identify and manage for the experiment). The benefits of the first strategy as well as getting some estimate of robustness. In industrial experiments, I seldom use more than 2 "exaggerated" blocks as we don't want to model a non-linear (e.g., quadratic) block effect (it is non-sensical).
- If you have a good relationship with the supplier, you could have them experiment on factors associated with making the batches and then do split-plots on your design factors (Batch experiment in the whole plot and your design factors in the sub plot...very efficient and effective). The most information for the least resources.
"All models are wrong, some are useful" G.E.P. Box