The way I know is a little janky, but give it a try. 3Shape is mainly looking at file names, not what the scan actually is, so create a dummy order, scan something in, replace the scan files with the files you want converted. You must do this correctly for it to work. I'm going to give you a step by step, but may still be confusing, feel free to ask questions.
1. Create new order and scan some generic models just to get through the scan phase and populate the folders
2. Right click and navigate to "advanced" "explore order" on both your new generic order and the order that you need to convert scans for
3. Open the "AuxScanDir" on the order that you need to convert scans to .stl
4. Open an additional file explorer window to an empty folder, I would recommend just creating one on your desktop
5. Ensure that you don't get the 3 folders you have open mixed up
6. Copy the files from the auxscandir that you need to convert to the new empty folder
7. Open either the "upper" or "lower" folder of your generic scan
8. Copy the name of the file within that folder (depending on which you open and your setup, there may be two files within the folder, do this one at a time)
9. Go to one of the files that you previously copied and rename it with the file name you just copied
10. Copy and paste your renamed file into the folder that you copied the name from
11. You will be prompted that there is another file in the folder with the same name, select "replace existing file"
12. Repeat this process until you have renamed and pasted all files needing to be converted
13. There is a small chance that you will also need to do this with the "AuxScanDir" of your new folder as well, if you do, ensure that the scans renamed and placed match the files in the upper/lower folders. I would skip this step on your first attempt, I just wanted to let you know that it could be a factor.
14. Once all files have been switched close your folders, go to your generic case that you pasted all the files into. Right click go to "advanced" and "export scan" switch to stl. and export, it should export the files you are trying to convert into an stl. f you did everything correctly
As mentioned in 13, I'm not certain if 3Shape uses the auxscandir at all when exporting scans, if it does you will have to replace the appropriate files in there as well.
Hopefully this helps!