This may or may not be related to this solved bug report:
Annotation Order - Reverses after "export" (https://www.photools.com/community/index.php/topic,14730.0.html)
...but the behavior described there happens also when copying Face Annotations between files in the Viewer.
If we have File-1 with Face Annotations like this
..........
.......... : : ..........
: : : 2 : .......... : :
: 1 : : : : : : 4 :
: : :........: : 3 : : :
:........: Person-B : : :........:
Person-A :........: Person-D
Person-C
...and we Copy them from this file in the Viewer (Ctrl+C), and navigate to File-2 and paste (Ctrl+V), the Annotations themselves stay in the same relative order, but they're now numbered in reverse:
..........
.......... : : ..........
: : : 3 : .......... : :
: 4 : : : : : : 1 :
: : :........: : 2 : : :
:........: Person-B : : :........:
Person-A :........: Person-D
Person-C
The PersonInImage Tag reflects the right-to-left order in File-2. After a write-back (and the regions are created), the PersonInImage Tag still reflects the right-to-left order (i.e. it follows the Annotation Numbers), but the newly created RegionName Tag reflects the "correct" left-to-right order (i.e. it follows the Annotation Labels).
I wonder if this might be what accounts for the:
File [n] face [n] has a mismatch in face/anno sort order
...diagnosis warning?
This has been fixed for then next release. Thanks for reporting it.