If you right click in the background and save the whole scene as an STL, then you can just import the whole scan as a jaw scan if you "break" the link with the current scans in the CAD-Data folder. You do this by renaming them so they do not match the .dentalproject file naming convention.
Alternatively, if you look in the CAD-Data folder, you can see the dies numbered in FDI numbering. If you swap the numbers around so that the ones mislabeled are correct, then when you relaunch CADApp and choose to load from Scan Data, the files will auto pull the correct order.
Lots of skinning in Exocad! I prefer in Medit scan to set up the scans to export as one piece, instead of dies separately for this reason though. Even the most careful scanner will oops sometimes. The only drawback is that when you go to mark margins, sometimes the tissue (if you have gingiva, or if you scan a solid stone and scan in dies for margins) can get in the way when marking your margin. As long as they're ditched well though, when you detect it Exo picks it up really well.
Apostolis159 probably has a scanner that auto-exports as one solid file instead of labeling the dies in exocad format, or has it set to do so in Medit scan