The APM 12.6 DVD contains two BIAR files - Allegheny_r1_Reporting.BIAR and CA_ITAM_Reporting.BIAR. What is the difference?

The Allegheny_r1_Reporting.BIAR is the original BIAR file with only APM reports.
The CA_ITAM_Reporting.BIAR file includes both APM & SWCM reports and this is the file the installer uses to import the reports. If you are manually importing reports, then use the CA_ITAM_Reporting.BIAR file for import.