I kept re-running scans and identifying the plugins that were causing BIAB to crash and adding them to the exclude list (the two biggest issues were with DD Delay.dll and BIAS Pedal_x64.dll). Now finally, the scan runs without crashing, but the scan log is full of errors. At least I got Waves Abbey Road Studio 3 back, however, per the OP, BIAB does not retain it after I close a project.

Thank you again for your help.