Dear Sir/Madame,
This should be possible but the amount of changes required cannot be explained here and this is not covered by technical support. You probably want to purchase an engineering/integration support contract from 4DSP, then we will be able to help you down to the details.
The first thing you need to do is making sure both FMC150 channels are phase aligned otherwise you cannot reconstruct your final buffer. There might be some difference in the channel amplitude because physical aspects. So you also want to check the integrated circuit manufacturer to understand whether or not one can compensate for amplitude (maybe gain/offset compensation). If that does not exist then you might want to design a front end PCB able to calibrate both input.
Then you need to make sure the firmware can buffer both channels in the same time, same clock domain.
I hope that helps!
Best Regards,
Arnaud