What a relief! The broken slides were scanned completely and they came out great (sometimes the focus maps get off and tiles of the image can become blurry, but I checked all the tiles and they are sharp!)
The techs are flying in tomorrow to fix the unit and, fingers crossed, we'll be up and running soon. I'm going to scout around for some slides I don't care about to use before putting actual data in. I think starting with blanks will work but something that will generate an image, but won't cause weeping if they end up broken, is the second step.