It’s good you take health warnings seriously. However, the warnings over Flaxseed, to me, have picked up a bit too much negative traction. The NFA simply warned that, because ground flaxseed can produce hydrogen cyanide and they don’t know the amount consumed to cause negative effects, they recommend not consuming it at all. From the NFA statement (translated into English):
There is not yet enough knowledge to say how much crushed flaxseed to eat without the risk of damage to health. Therefore, our advice is not to eat crushed flaxseed.
They even say there is a very low chance of getting Hydrogen Cyanide poisoning from flaxseed (if there is a real risk at all):
If one were to ingest high doses of hydrogen cyanide at one point there arises the so-called acute poisoning symptoms. However, it is very unlikely that you get in such a dose over crushed flaxseed. Acute poisoning symptoms can include headache, nausea, dizziness, confusion and numbness. Serious hydrogen cyanide poisoning can affect breathing. There are no published reports of acute hydrogen cyanide poisoning caused by crushed flaxseed.
It’s good to be aware of the warnings, however, to me, this is just a warning to be safe.