I believe the rested bonus only effects monster kills (or crafting, or gathering) and only at a rate of 50%. For example, when crafting, HQ% also provides you with an experience bonus. Bonus exp that comes directly from the HQ level itself, does not chip into your rested bonus. Only the 50%(or whatever it is) of the base amount is what's chipped away.

This is why you can suddenly find yourself with a blue bar, when before you didn't have one.

Thanks,