The where clause of the wizard is wrong and should use "not like replaceFile" instead of "like replaceFile".
This will be fixed in master with https://review.typo3.org/#/c/49452/, but 7.6 should receive a dedicated bugfix for this issue.
[BUGFIX] FilesReplacePermissionUpdate wrong where clause
The where clause to check for updates should select
records that have writeFile set, but not replaceFile.
Reviewed-by: Benni Mack <email@example.com>
Tested-by: Benni Mack <firstname.lastname@example.org>
Reviewed-by: Christian Kuhn <email@example.com>
Tested-by: Christian Kuhn <firstname.lastname@example.org>