You seems to be familiar with folders so let's try this:
Run the game as normal until they ask you to swap disks. At that point, tab out of DOSBox and do this in Windows:
(I will use Folder1 for your Wizardry 1 folder and Folder2 for your Wizardry 2 folder.)
-Rename Folder2 as Folder3. (use whatever name you want, it won't matter)
-Rename Folder1 as Folder2. (use the exact same folder name you used to mount Wizardry 2)
Tab back in DOSBox.
Once this is done, hit enter so the characters are "being transferred". By transferred I am pretty much certain that it means "loaded in memory", so it should have no effect on either folders.
Once the game tell you "[character] was transferred.", do this:
-Rename Folder2 as Folder1.
-Rename Folder3 as Folder2.
And you should be back to normal folder with characters hopefully transferred.
Let us know how this work.
