The cause: Recent changes in AROS boot code made the contents of file S:hidds.prefs obsolete, and VmwUpdate ignores this file while updating the others.
The workaround: manually copy S:hidds.prefs from the nightly build CD to your drive's S drawer before or after VmwUpdate has sone its job, but anyway before rebooting AROS. If you have already reboot and got your VmwAROS installation unusable, please boot your system with the newer nightly build and do the manual copy of the file.
The solution: please wait for an updated version of VmwUpdate and use it instead.
Thanks to Pavel Fedin for helping me to fix this.