That's why each item has its own power switch, or in the case of the EFIS, a key sequence to force a reboot. With modern electronics the Avionics Master switch is unnecessary and is nothing more than a single point of failure for every item powered through it.
The worst problem you might see is an EFIS reboot during engine cranking. That's easily addressed with a small backup battery like the TCW Technologies IBBS or the EarthX ETX104. Dynon has their own EFIS backup battery; perhaps Garmin has one too.
If you haven't done so, I'd recommend reading Bob Nuckolls' book, The Aeroelectric Connection. Bob's current state-of-the-art design for an E-AB aircraft with an electrically dependent engine is his Z-101B. Review the diagram, read the notes, and feel free to ask questions, either here or on the AeroElectric-List forum.