The virtual output directory can be changed in an admin connection to an ArcGIS server in ArcCatalog. This change should be applied automatically to all services that were defined to use the previous virtual output directory. For geodata services, however, the change is not being applied and this is a software defect.
This can cause operations on a geodata service to fail, since the old virtual output directory may no longer be valid. For example, creating or synchronizing a replica may fail with an internet connection due to this problem.
This is a software defect.