The flaxseed is used in such a small amount, strictly to provide a really nice chew to these tortillas. I find I much prefer this result vs. just straight cassava flour without the ground flax.
These tortillas will work without the flaxseed, you may just need a little less of the liquid than you would when include the flax. I haven't tested ground chia seeds myself, so I am not sure if those would provide the same results. If you experiment and try it, please report back.
For AIP, leave out the ground flaxseed
This is the tortilla press that I use:
http://amzn.to/2jvuw5q