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For the first time in years, I played SoD again and finished the first campaign for each character. I carefully built up my heroes and made they sure they have the skills I would like them to have.

After I started Gem's second campaign, I noticed that her skills seem to be randomised and I now have useless skills like Eagle Eye and Navigation! This seems to be the case for all of my four heroes. I tried reloading and got a different set of skills, but they are still randomised and I'll probably have to spend hours restarting the campaign before I have my skills back.

Any way to fix this?
There isn't. The best you can do is to simply reload until most of your heroes have most of the important skills. The bug shouldn't be too much of a problem anyway, since heroes carrying over between missions tend to break missions anyway. I never played on a difficulty level above Hard until the Shadow of Death campaign where I had to bump the difficulty up to Impossible or give myself some other handicapping rules to abide to because when you start a mission with Fly, Dimension Door, Town Portal or the Cloak of the Undead King, and you can teleport in front of the enemy castle and conquer it in the first week if you so desire, there's nothing the game can throw at you that you can't prevent or survive. Missions just weren't designed for that kind of power on day one.
I tend to take might heroes over magic heroes and don't cheese the game with spell anyway, but this is just a massive downer. I carefully levelled my heroes and now I'm stuck with Learning and Navigation. They should have lowered the level cap instead, no passive-aggressively weaken your hero.
Might heroes are so much better than magic ones, but, a Might hero that dab into magic is so much better than one that doesn't. And, even when you play a barbarian, the mightiest of the might heroes, you'll be offered the chance to pick up one of the four school of magic once every four levels, and you will be offered the chance to pick up basic wisdom once every six levels. Even if you don't intend to use Dimension Door or Town Gate, spells like Resurrect, Mass Haste, Mass Bless, Mass Slow, Mass Shield, Mass Prayer, Mass Dispel... all of those spells have the potential of turning a defeat into a victory when used correctly, and shouldn't be ignored.

But, I cannot say how your heroes new skills are right now, I recall that in my game, Crag Hack and Yog both had, Offense, Wisdom, Air, Earth and Logistics. Gem had no Logistics but she had Wisdom, Air, Earth and Water. As for Gelu, he had Logistics, Earth and Water. I forgot what were their other skills, I recall that I tried to reroll to get more perfect skills but in the end I settled for those skills, and as soon they learned Dimension Door, Town Gate, Resurrect, and the standard buff and debuff spells, Crag Hack, Yog and Gem went on earth conquering rampages teleporting all over the place, and Gelu who, had no access to the Dimension Door spell, just stayed behind, recruiting troops and defending the castles. And, although I felt like the game screwed me over, at no point I felt like I was at a disadvantage, quite the contrary, the maps still felt like normal maps, maps where you start with low level characters and no spells. Even when you ignore the game breaking spells, being able to clear most monsters around your starting area with nothing but damage spells is tremendously broken. And so I felt the need to pump it up to Impossible difficulty to help the AI a bit.

But all in all, I know that it sucks but, due to the very nature of the carry over feature of Heroes of Might and Magic III, even if you get a couple of useless skills on your heroes, you'll still have a massive advantage over your AI opponents for the rest of the game, and this, even on the hardest difficulty level, if you were worried the screw over would affect your chances of victory.
I think they should have stuck with the RoE concept (heroes carry over between scenarios, not campaigns) or the HoMM1/HoMM2 concept (heroes don't carry over at all) and don't make the protagonists heroes (like in RoE, where you don't play Catherine herself).