I was under the impression that if the reformation never happened, the game would eventually skip over to the Age of Absolutism. Is this wrong?
In case I'm wrong, I can see two possible solutions. The easiest is to simply have Chalcedonian convert to Catholic. If you want more nuance, you can introduce a "clean-up" decision available after 1444 to convert all Chalcedonian provinces and characters to either Catholic or Orthodox, depending on if the church is Latin or Greek.
The other solution is unfortunately much more involved. You could edit the reformation-related files to let it work with both Catholic and Chalcedonian religions. This would mean editing all the relevant event, decision, and mission files and placing them into the converter, which as you would imagine would be a lot of work.