Typical now I have asked the question I have thought of one solution and found another work around in the forums.
Kovid gave one solution to an earlier query:-
sure, I'm not going to add support for that to the GUI. But you can achieve it yourself by managing the conversion subfolder in the calibre config directory. That's where all conversion defaults are stored. Just have multiple copies of that folder and rename the need copy to conversion each time before launching calibre.-
I came up with another which is to install Calibre Portable and point it at the library I intend to store my Kobo ebooks. The conversion settings of this Calibre install are set up with the settings I need for my Kobo and do not interfere with may main Calibre installation, whose conversion settings suit my COOl-ER. I will use one install or the other and not open both at the same time, which should prevent any clashes between the two.
I will also use Kovid's work around on the portable install for the other sets of conversion config settings I need for the conversions I do for family and friends.
HTH