In my case, it never got better, even after two weeks, it only got worse (to the point I passed out at least on two occasions, and came close to passing out on many more).
Unfortunately, because the possibility was never mentioned in the book, I just assumed the whole diet was stupid and dangerous (at least for me).
I eventually discovered (like 20 years later) that in my case the "flu" was caused by rapidly dropping blood sugar (not always, but usually into the hypoglycemic range).
All I needed to fix the problem was to move onto OWL and find the carb level at which symptoms disappeared. I never really thought about it until my current doctor, several years ago suggested that I try low-carb, but warned not to go "too low," admitting that he had no idea what would be too low. So for the first time, it dawned on me to experiment with carb levels to find the point at which symptoms disappeared (or where at least manageable) and yet allowed me to lose weight consistently.
So, if your symptoms go away at 2 weeks or before, that's absolutely fantastic, but if they don't (or even if they get unmanageable before the 2 weeks) at least consider moving on to OWL before deciding to ditch the whole low-carb option (as I foolishly did).
Hubby and I went to a weight loss clinic for an evaluation (unfortunatley our insurance didn't pay for the program and we couldn't afford it - when we saved up enough money for us to do the program anyway, the program had been discontinued).
Hubby because of his diabetes and diabetes meds (he was on pills and injectable meds), he was encouraged to "do Atkins backwards," that is moving down the carb ladder backwards first replacing grains with whole grains, then reducing carbs 5 to 10g per day...). This was so that he wouldn't end up in severe hypoglycemic shock.
I was told I could do South Beach, Atkins, or even "backwards Atkins" if I wanted.
I'm not suggesting that you modify Atkins if you don't absolutley have to, just that a modified Atkins is better than no Atkins at all. Don't throw the baby out with the bathwater as I did.