The Boss stones may, as others say, be an exception and nothing is certain. But I am following and have successfully used the mod: Upgrade_World by JereKuusela.

As it does exactly what the OP is asking (so far) then can be uninstalled with its changes remaining.

Yes it by default allows for builds on areas that with new updates that have been built on.

Obviously a full biome upgrade will be a major test of any Mod like this so keep exploration (or even close journeys near) Mistlands to a minimum to avoid what issues you can.