Yes, it does
On page 62:
Your Endurance rank determines your Health, which equals 3 × Endurance.
In other words, if a flaw affects your Endurance rank, it affects your health too.
Flaws, in general, always affect your passive result (normally rank * 4), so all secondary abilities are affected by a flaw in that primary ability, including Combat Defense and Intrigue Defense.
When you gain this drawback, select a single ability. You take –1D on all tests involving this ability. For how these flaws might manifest in your character, see the following chart. When calculating your passive test result with this ability, you treat your ability as being 1 point lower. For example, if you have Perception 4 and the Flaw (Awareness) drawback, your passive Awareness result would by 12 ([4 − 1] x 4). You also reduce any derived characteristics (such as Intrigue Defense or weapon damage) by 1.
That -1D denotes a Penalty Dice (page 31), which means you must subtract an additional dice from your checks. Example, you have Marksmanship 4 but also got Flaw (Marksmanship), that means you roll 4 dice, but have to remove one dice from the result of your checks.
But keep in mind that penalties don't reduce derived stats, that is a wording exclusive to Flaws. So if you take a -1D penalty from wounds, your Health, Combat Defense or Intrigue Defense is unaffected, but on any check you will have to remove one dice from the result.