While I fully understand the desire to be able to swap the fridge to either set of batteries, I have to question whether the option is worth the effort/cost/potential pitfalls.
Did VF say there was no issue switching on the fly between 12 and 24, or Danfoss/Secop? Are you sure they understood your question? Was it an actual tech, or a applications/marketing 'engineer' who is trained to read the same manual you can find online which clearly states it can operate on 12 or 24 volts DC?
What I do not like is how the danfoss Electronic control unit manual say the maximum voltage for a 12v system is 17 volts. How is it supposed to know when it is switched from one to the other? If there was no issue, and it could switch on the fly from 12v to 24v, then I do not think there would be this 17 volt warning. I am no electronics guru, but this raises a red flag to me.
http://files.danfoss.com/TechnicalI...nit_101n0600_12-24vdc_08-2011_dehc100m602.pdf
I imagine there would have to be some sort of stress on the components inside the compressor controller switching like that. If it works as intended without the magic smoke escaping on the first switching on the fly, They'd likely last the warranty period, no problem, and after that neither VF or danfoss shives a git. I'll ask my electronics repair contact about the switching stresses on internal components but a response could be days away.
How often are you likely to switch power sources?