Excellent, thanks for your reply!
Do you have any clue what format the Onyx makes the layer in? Apparently PDFs have a bunch of different options (despite Adobe claiming they're standardized). I've tried the flattening options in mac (preview and safari), but they don't catch the Onyx's layer. Adobe recognizes it, but I don't want to spend ~$200 on adobe pro if I don't have to. So if I know what type of layer I'm looking to flatten, I may be able to find a specific solution.
Thanks again.