The /usr/sbin/vrpm utility has been created to ease those updates. For example, say you have 4 vservers v1 v2 v3 and v4 and 3 packages a.rpm, b.rpm and c.rpm to update. You do:
vrpm v1 v2 v3 v4 -- a.rpm b.rpm c.rpm or vrpm ALL -- a.rpm b.rpm c.rpm
The last command will apply the updates to all your vservers, one after the other.
Now, after performing this steps, you end up with 4 vservers updated independently. The disk space is not unified any more, for those 3 packages. To regain unification, you do:
/usr/lib/vserver/vunify v1 v2 v3 v4 -- a b c
vunify may be use any time.to re-unify vservers. You may want to run it after you have performed major RPM updates.