So just started a new run of QFG, this time with all characters, and finished up 1 just fine. Went to import all 3 character saves to 2 and discovered that both the Magic User and Thief have suddenly changed into Fighter classes? Equipment and skills are the same, just that their classes have swapped, which I know can have repercussions in future games.

Tested it out with my old Anthology CD copy and import worked fine. So I think this is likely a bug with GOG version itself.

Anyone else experience this? If so, what did you do to overcome it?

This can happen throughout the series, even in the original release versions. You can find character editors online to correct it.

Here's a link to the patch http://sierrahelp.com/Patches-Updates/Patches-Updates-Games/QuestForGloryUpdates.html

Just scroll down to Quest For Glory ii and download Quest for Glory II Character IMPORT Patch (QG2IMPRT)

this helps if your using dos box.

Even with the patches it still happens sometimes. For some reason they couldn't just keep track of the class, but inferred it from your skills.

Does ScummVM also have this problem?

This bug is automatically patched on-the-fly by ScummVM itself, as well as a few others.
No need to install any patch files.

For example there is also a Saurus bug, that may soft-freeze the game.

See here:
https://github.com/scummvm/scummvm/blob/master/engines/sci/engine/script_patches.cpp

[x] When the player encounters an enemy in the desert while riding a saurus and later tries to get back on it by entering "ride", the game will not give control back to the player.
[x] The Jackalmen combat code has at least one serious issue. ... Some variables will show that there is still an enemy, while others don't. The game will crash when leaving the room. The original interpreter would show the infamous "Oops, you did something we weren't expecting..."
[x] Quest For Glory 2 character import doesn't properly set the character type in versions 1.102 and below, which makes all imported characters a fighter.
[x] On day 27, approaching the Emir's palace at night without a visa crashes with a missing text error.

It also fixes other bugs for the other Quest for Glory games, especially for the well known buggy QfG4.