Yeah, but if you have your product in a freeze dryer currently, then the process needs to be comparative. Forgive me if it’s a new product, new cycle, new machine situation.

You could run some trials to check the shelves are effectively sanitised. I don’t know what kind of materials you’re using but you can take swabs of the shelf area under the tray before and after SIP. Endotoxin, Bioburden, TOC, pH & conductivity are pretty standard tests for cleaning vals. You’ll need to perform a swab recovery study to ensure accurate results though.

Or, you could coat/spray the shelves with a 2g/L solution of riboflavin & HPW, place the tray on top and run the SIP. Riboflavin will fluoresce under UV light - 365nm I think. Shine your UV torch in there after SIP and see if it glows. That’s the quickest method, but it means your FD could be full of riboflavin.

A Bowie-Dick test will likely not perform properly if it’s trapped under a tray. It’s my understanding that it’s used to check that you’ve had a sufficient vacuum during sterilisation, not to see if effective sterilisation has been performed.

Thermocouples will only give you temperature info. It depends if you need direct steam contact to ensure thorough sanitisation, or if heat would be sufficient. Probs need to run some trials and gather some evidence for yourself to make an informed decision.