Switching from polyethylene to polycarbonate sounds straightforward, but it can lead to a perennial problem: milky mouldings.
Instead of getting crystal-clear polycarbonate parts, you get cloudy, opaque mouldings.
This can easily be avoided, by ensuring that you shift all traces of PE from the machine. Once you've moulded all your PE, run through a few kilogram's of Barrel Blitz Universal, before feeding polycarbonate into the hopper.
A word of warning here: some purging agents use PE as the carrier, so they'd never work here. Because it's neutral, that won't be a problem for Barrel Blitz Universal.