[MOD] Scenarios and campaigns: original, Hammers of Fate.

This is quite an unpleasant flaw – in the fort on the hill, you cannot retrain creatures from the main upgraded version to the alternative one, and vice versa.

Either it's configured this way, or something else, I don't know... Some of the Lords of the North missions are tied to the red tier of the Order faction, which in this game was not an alternative to the main one, but a new, quite overpowered line, only for the campaigns. Apparently, the forts somehow "know" this, but the cities don't. And this can be worse in terms of completing the campaigns (although I don't think there was a moment where it was crucial).
If you need to fix the forts, you need to tinker with the maps. Most likely, this is in the fort settings. But I would rather make a restriction on the availability of upgrades in the cities in the campaign (each city has such a setting).

There is one problem: assembled artifacts are not carried over from mission to mission. Is there any way to fix this?

I think there is some way to do it. But again, you need to tinker with it.