There is probably a lot of valuable information buried in this forum. I found most of the information about problems and the unofficial patch here.
Here is a relevant tread I found:
https://www.gog.com/forum/warlords_battlecry_series/wbc_3_patch Invisibility of certain units was one bug but the most serious one was a bug that always made the random number generator always give you the same number, making spells much less useful and always giving you the same item in addition to other problems.
From what I've read this was never a problem with the CD version, it was existed only in the digital download versions given to GOG and other distributors.
At first GOG just recommended to install the unofficial patch, but since the state of the game was so bad they decided to include the unofficial patch with the game you bought. This was a good choice at the time, but it quickly became controversial because the unofficial patch is by definition a mod and the other changes of the game, like thee nerf to summoning units was not made by the original developers of the game.
GOG then later reversed the game back to the state it was in before, but managed to fix the bugs themselves. This just one of many episodes which shows GOG's great care and dedication to make the games they sell the best they can be. I doubt that you can find any other game download distributor who goes to such great lengths as GOG do.
I prefer to play this game without balancing mods. While the makers of the unofficial patch probably are right that summoned units is very powerful and can be abused, it is not a problem for me since this is a game I only play myself or with my brother. So if anythings is to overpowered we can just try something else instead.
By design this game seems to give you a really wide variety of options to explore and it isn't as concerned with balance as most modern strategy games geared for online multiplayer is.
legraf: Ah, this does sound correct from what I see now. It's true: I have version 1.03.24, from back when that was what GOG provided (WBC3 was the first game I bought through GOG!). Sorry for my misleading information then.
So, the version now available here is plain 1.03, but with some additional fixes - are those documented anywhere? My game runs so well I'm not inclined to risk any changes, but if I could read a changelog I'd consider it!
Ah now I understand your original question. I must have read it a little too fast :) I haven't ever seen those changes documented by GOG anywhere. The sticky post at the top only mention invisibility. I assume that they only fixed those critical bugs and nothing else. Thus your version of the game is no worse, it just has the balancing and extra features of the unofficial patch applied.
If I were you I would not reinstall the game but rather keep the install along with the progress and heroes.