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A great troubleshooting tip...."When you eliminate the impossible, whatever remains, however improbable, must be the truth." Sir Arthur Conan Doyle
Any supplier worth his pay will advise you on processing parylene.
As I recall, it's toughness, and relatively poor adhesion to some substrates, makes it difficult to remove whatever the masking material is without disturbing the coating.
If volume allows, you may want to consider a contract coater. Or is that what you are? Get your supplier involved!
BTW, while it's transparent to visible light, it filters Uv light.