Hi Shanti - see discussion here, I think this is still difficult to do in cryosparc: Merging two data sets with different pixel size
You might try taking extracting both in the same box size (in Å), and then resampling one stack so both are the same box size (in pixels). Unless this results in identical pixel sizes though, I suspect it might still give an error. Prob better handled in relion for now.
Oli