Both are TIFF files. That said, TIFF is a very flexible format and it's used for a wide array of things across many technical disciplines. It's hard to say what a MxNx2 image is inteded to be. A 2-channel image might be interpreted as volumetric data, or in other contexts, it may be a monochrome image with alpha.
If we assume that the two channels represent comparable quantities (e.g. visible light intensity), then you could choose perhaps to simply average them.
A = imread('fileA.tif');
A = mean(A,3); % average both channels
imwrite(A,'fileA_modified.tiff')
Or you could do any number of other mathematical operations to reduce the two channels to one (e.g. max() min()). Alternatively, you could just pick one of the two channels if one has some particular significance in your context.
