Take a .odb created with ObjectDB 2.7.2 or later OR EARLIER. Run ObjectDB 2.7.2 Doctor on it. See indexing errors reported.
Run ObjectDB 2.7.1 on same .odb and you will not see indexing errors.
Run ObjectDB 2.7.2 (or later or earlier) Doctor with repair and create repaired.odb. repaired.odb will still show indexing errors when ObjectDB 2.7.2 (or later) Doctor is run on the "repaired" database.
Automatic index rebuilding ("<index-update enabled="true" priority="40" />") does not correct the database.
So, in summary, I think ObjectDB 2.7.2 (and later) Doctor is incorrectly stating that indexing errors are present.
(I am running this test with a java.exe that is Java 9, though I don't think that matters since ObjectDB 2.7.1 Doctor does not show any indexing errors.)
Here is an example output from my .odb:
C:\Users\BoydE\Desktop>java -cp 2.7.2_03\bin\objectdb.jar com.objectdb.Doctor C:\Users\BoydE\MoxyDox\ObjectDb\Test.odb ObjectDB Doctor [version 2.7.2_03] Copyright (c) 2017, ObjectDB Software. All rights reserved. Scanning the database file... 2MB (total) Analyzing database structure... 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Index Errors ------------ [1] Index com.unilogical.moxydox.protocol.server.jdo.JdoEntityId[id] requires rebuild. - missing entries: 7 - extra entries: 7 [2] Index com.unilogical.moxydox.protocol.server.jdo.JdoEntity[idLowercase] requires rebuild. - missing entries: 16 - extra entries: 16 [3] Index com.unilogical.moxydox.protocol.server.jdo.JdoImagePageBackground[checksum] requires rebuild. - missing entries: 1 - extra entries: 1 [4] Index com.unilogical.moxydox.protocol.server.jdo.JdoImagePageBackground[location] requires rebuild. - missing entries: 1 - extra entries: 1