I've removed a chamois from a pair of shorts, very carefully, but haven't sewed one back in. I think you could cut a chamois down, you'd have to stitch around it to neaten the cut edges. As for sewing it back in, I think it would be smart to hand stitch it roughly in place first before overstitching with a machine, so that you avoid bunching and overlapping of the shorts fabric - you'd need to be rotating the garment as you stitched around, it could get very messy. But I agree, i think it's doable.