Although we haven't tried it with ground Flaxseed we will say yes. :) You will probably get a better texture of cracker and possibly a quicker drying time?!? Time to get out the pestle and mortar to find out. As for the unground seeds not being as healthy. We suspect that it will be because if you eat whole seeds there will always be those that your teeth don't crush so they will pass through your digestive tract intact, thus not giving up their nutrients.