Hi André thanks for the answer - it really helped.
I did a Shift-r and it came up with: "Failback not allowed when upgrading" "Press enter to boot" and it then booted up saying that the hypervisor was now build 800380:
~ # vmware -v
VMware ESXi 4.1.0 build-800380
However, given that the original error occurred within seconds of the patch update attempt, I didn't believe that it had actually worked (normally it takes a few minutes to apply a patch), so I then did another Shift-r to load the older hypervisor and this time, I was finally back to where I wanted to be:
/usr/lib/ipkg # vmware -v: VMware ESXi 4.1.0 build-502767
/usr/lib/ipkg # esxupdate query: ESXi410-Update02
Yay!
So, finally, I did a vihostupdate.pl to bring it back to Update 03 properly (this time taking a few minutes giving me confidence that it had actually done something).
~ # vmware -v
VMware ESXi 4.1.0 build-800380
~ # esxupdate query
---------Bulletin ID--------- -----Installed----- -------------Summary---------- ---
ESXi410-Update03 2013-07-20T10:26:17 VMware ESXi 4.1 Complete Update 3
Solved!
Once again, many thanks.