It would be an internal switch Mike, that I as the only only user of this thing, would know to change BEFORE the supply was turned on.
That kind of thinking is generally what leads to letting the magic smoke out -- always assume you will forget and do something stupid. Also, I am not sure you see Mike's point: unless the variac wiper is set exactly to 1:1 engaging the bypass will create shorted turn(s) on the variac. This will lead to a large circulating current through the wiper. If you are only a couple of turns off, this will create unwanted heating of the core and the brush. If you are off by more than that, it will blow the secondary fuse.
You are right, I was missing his point. I am glad I posted, I had a feeling it was all too easy...
I will try and source a suitable changeover switch. The original single phase supply had a 40 amp main input trip switch, so I need something that will handle about 40 amps when it is feeding the HV transformer direct and it sees full load. If run via the Variac a much smaller current draw would be made, as it would be feeding a much lesser load, so the 25 Amp limit of the Variac would be respected.
The infamous Ebay didn't show anything obviously suitable, especially if I try and find the ideal make / break / make type. I am in the UK, same as Mike, by the way. Thanks for stopping the magic smoke getting out