I doubt it
If you are not feeling it in the knee or in the muscles that connect the upper and lower leg, I can't imagine you are risking damage to your knees at all. There may be stress there, but it probably isn't much if you aren't feeling it directly. However, as described below, some stress in the upper-leg muscles would amplify whatever stress your ankle is subject to.
Here's a question. If you are barefoot does the problem go away, or at least get better? I ask that because most shoes, even flexible ones, transfer the contact point between your foot and the bottom of the boat away from the instep (the load-carrying part when kneeling barefoot) to the toes. The extra "lever arm" along the length of the foot when the contact point is the toes increases the stress within the ankle, and I experience that myself with certain shoes, where the same load creates more stress within the ankle (while extending that joint as far is it will go) if applied at the toes than if applied very close to the ankle itself (instep). The purpose of ankle blocks is to decrease the length of that lever arm and ideally not even force the ankle into full extension. However, as pblanc pointed out earlier, if the load applied to the foot is greater than it should be on account of a "tight kneee", ankle blocks will also make the knee slightly tighter so they may not fully cure the problem. I would not discount the possibility that your knee has a natural tendency to "spring open" on account of not enough working length in your quads, but you can figure that out better than we can (and if that's the case, this is the situation that can be cured by flexibility training).
It's all "lever mechanics", so it would be really simple to understand once all the factors are identified. We just haven't positively identified which potential factors are causing this.