I've covered this in a few other places, but this is a shortcoming of the GNS 530/430's hotswapping system. I've made several attempts to fix its code myself, and I've requested that Working Title look into it several times, as well. Unfortunately, I can't claim any progress on either end. I'm sure this is frustrating. Tt's not a feature I use myself, but it bothers me when the issues are out of my control to fix. I can try to make some headway with Working Title again next time I'm in contact with them, but that's where things stand right now, unfortunately.
I will add one more insight, just in case smarter people than I are reading this and want to attempt a solution. I found that the flight plan would be retained through any power-cycling of the GNS units if another native flightplan-linked interface was open, such as the PMS GTN. You can also try it with the MSFS VFR Map in the default C172.
VFR Map closed:
GNS Off -> GNS On -> Flightplan lost.
VFR Map open:
GNS Off -> GNS On -> Flightplan retained.