I have a situation where I can put 99% of my structured data into JSON-LD in the of my product pages. But the only way I can get the UPC is to place it inline as microdata.
Will Google aggregate the product data from the JSON-LD and the inline microdata?
Most likely yes.
Google’s Structured Data Testing Tool works fine if you are using JSON-LD and Microdata (and RDFa).
Google does not say otherwise (they did in the past), see their Structured Data Policies:
Some of Google’s structured data features are (currently) only documenting JSON-LD (for example, TV and Movie Watch Actions); for others, Google recommends using RDFa/Microdata, see for example their "About schema.org":
It wouldn’t make sense for Google to restrict authors so that can’t make use of all the features (using different syntaxes) in the same document.
That said, you can never know for sure (their documentation is not always up-to-date, and their rules might change each day.)