Tested version: 6.12
From Artifactory 6.4 metadata files are no longer being replicated and will be calculated by the target instance itself.
In case deleting the "repodata" folder from the source Artifactory it will deleted from the target Artifactory as well. However, in case triggering "Recalculate index" on the source the metadata files will be generated on the source only and on the target side only the "repodata" folder will be created without the metadata files itself.
To resolve this behavior it will be required to trigger "Recalculate index" on the target instance.
As metadata files are not longer being replicated it should not be deleted as well following the replication process or otherwise regenerate in case of deletion.