I guess the folder was still there because I had stored the setup facility in it. Otherwise it would have been total replacement I guess. And yes I'm having to update manually on the first day. I've scheduled update / scan tomorrow morning so see how goes.
Off topic / I've got some other problems on this computer - to do with outdated software that has got in the way of things - to the point that an infection slipped in. I've tidied up okay but I'm going to have to do away with IBM toolbox, which wants to operate in real-time but isn't supported by the service link now provided. I have the programs disabled at the moment, including a general software organiser program from Software.com that sorts updates, downloads, and drivers etc...from what I can tell - also interactive, and also in thick of things when malware slipped through. The actual event -- a request for update from IBMAccessSupport, the control program, that timed out because the destination service has now become something different.
I seem to have everything back to normal now.
avast picked up the malware in a scan. I've still got MSE and avast running side by side. But like I said above, I have to put paid to the outdated IBM software before I can freely watch the AVs run.