How many hours after eating, was that bonk?
What are you eating nowadays?
What is your exercise program, daily and weekly?

It does sound to me like you ran out of glycogen / glucose.

If you're at Atkins induction level of carbs, and you're doing something every day like strength training and long bike rides, your body might not be making enough glucose for your exercise needs, yet.

it could be a matter of waiting for more adaptation, OR
you need more protein for gluconeogenesis, OR
you need more fat, OR
you need more slow carbs.

I like to think of the kinds of fuel as if fat were the gas in the car, and carbs are the spark plug energy. Exercise always needs some glucose as the muscle spark plugs. YOu need some to keep the engine running and since it's sparks, you really don't want more or less than you need.

In the case of a bonk, your metabolic engine quit. So how to make sure you have enough glucose in the spark plugs - that is, in muscle glycogen and the liver - for your bike rides?
I would check all three factors.
Make sure there's enough protein.
Make sure there's enough fat so you can spare glucose.
And make sure you replenish the glucose / glycogen burned in your exercise program. Either by having replenish days after intense exercise or having more than 20 g of carbs if you do it every day.