I just put my laptop to sleep on one network, moved over to another, and woke it up, and this caused me to lose 2 of my "universal" variables. If I look at my ~/.config/fish/fishd.originalhostname file it lists the variables but my ~/.config/fish/fishd.newhostname file is missing them.

Why are the fishd files specified on a per-host basis anyway? My only guess is so you can synchronize your ~/.config/fish folder between machines and keep separate fishd variable sets, but that would be far better served using some permanent hardware identifier instead of the hostname which is prone to changing.