That depends how the lights are wired. If you have a daisy-chained quad set of lights then you’ll only be able to control them all simultaneously, but if you have two pairs then it should work fine to connect each pair independently (via the Lights1 and Lights2 outputs).
I’d suggest taking a look through this post. Whether the differences are meaningful depend on your operating priorities. I suspect for most users the Raspberry Pi upgrade is the most significant part, assuming the current flight controller is still working fine.
That error can be safely ignored - the QGC version is just too old to know about the latest parameters, and that parameter stopped being necessary a while ago.