i maintain game various folders for different combo's of overhauls/versions of the games and combo's of mods; i do all this on my F: drive ~
F:\games\7 Days to Die\7.Days.to.Die.a21.2.(b37).Hotfix
F:\games\7 Days to Die\7.Days.to.Die.a21.2.(b37).Hotfix.with.Joke.Mod
F:\games\7 Days to Die\7.Days.to.Die.a21.2.(b37).Hotfix.with.Outback.Roadies.Mod
F:\games\7 Days to Die\7.Days.to.Die.a21.2.(b37).Hotfix.with.Preppocalypse.Mod
F:\games\7 Days to Die\7.Days.to.Die.a21.2.(b37).Hotfix.with.Random.Wandering.Hordes.Mod
F:\games\7 Days to Die\7.Days.to.Die.a21.2.(b37).Hotfix.with.Wild.West.Mod
F:\games\7 Days to Die\7.Days.to.Die.v1.0.(b316).EXP.b317.Hotfix.with.Guppy.Zombies
F:\games\7 Days to Die\7.Days.to.Die.v1.0.(b333).Stable
..i only ever play the game thru %appdata% ie thru Steam when i'm playing online with friends, and as Steam itself obviously uses %appdata% i don't mess with those files/don't add mods to that folder structure anyway, my point is that i don't believe my method of keeping separate game instances outside of %appdata% should be affected by whether or not the location of the mods folder changes