The FilesDataIntegrityService.checkFiles currently does not have the ability to gracefully handle situations where references to a file/files exist within the Files database but do not exist on the filesystem. The command's current behavior is it will not remove the entries for these missing files from the Files database table. Rather you will see the following error in the Files app systemlogs:
CheckDataInte E EJPVJ9812E: The required file identified by ID 00ebc6df-3b3d-4b00-9599-3fe4368ea43e (referenced in table "FILES"."MEDIA_REVISION" column "MEDIA_FILE_ID") was not found.
This enhancement request is to introduce the additional functionality that would allow the handling of such situations ie perform automatic cleanup of references to these nonexistent files from the tables.
The current behavior of the command is specified in the following product documentation:https://www.ibm.com/support/knowledgecenter/SSYGQH_6.0.0/admin/admin/t_admin_files_data_integrity.html