Inconsistencies after Bitbucket version upgrade

[landro]

After an upgrade from Bitbucket version 7.17.13 to 8.9.3 inconsistencies are detected:
“Integrity checks are complete and some inconsistencies were found Check the application logs for information on any restore actions carried out.“

 The application log shows dozens of errors as follows:

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2023-08-07 15:19:48,632 ERROR [Caesium-1-2]  c.a.s.i.i.DefaultIntegrityCheckReporter The repository ~FRUTT/golfapi could not be restored. An error occurred while working in directory /var/atlassian/application-data/bitbucket/shared/data/repositories/3896

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 and warnings

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2023-08-07 15:19:51,408 INFO  [Caesium-1-2]  c.a.s.i.i.DefaultIntegrityCheckEventService Auto-integrity checking found an inconsistency

2023-08-07 15:19:51,413 WARN  [Caesium-1-2]  c.a.s.i.i.DefaultIntegrityCheckReporter SSOR-ZAMP/ui-cat[2048]: The following 1 inconsistencies were found: [SSOR-ZAMP/ui-cat [2048]: The following pull requests are missing on disk: [56, 33, 56, 89, 91, 79, 70, 71, 72, 73, 74, 75]]

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Nothing has manually been deleted from the disk and the errors did not appear before the upgrade.
Is there a way to get rid of the errors by removing references to non-existing paths? If so, how?

Does anyone have a clue what might have caused the inconsistencies after the version upgrade and what the impact might be?