Have you tried upgrading the MDs through chroot on the core? Upgrading the MD on the MD itself will be extremely slow due to the network file system.
The other option, and likely the best, is re-running Diskless_CreateTBZ.sh on the core, setting the needs configure flag in the db for each of the Generic PC as MD devices, and then running Diskless_Setup.sh to recreate the MD filesystems.
iirc, nothing in pluto-confirm-dependencies will alter /usr/pluto/bin/Config_Ops.sh
J.