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This honestly and truly sounds like Lyme or Anaplasma to me. The two big symptoms your dog has: transient lameness in the limbs and the sudden onset lethargy are both huge red flags when it comes to diagnose these tick borne diseases. There's a website that outlines some of the symptoms here: http://www.provet.co.uk/health/diseases/lyme.htm
I know that she's been tested for Lyme, but I wonder if they tested her for Anaplasmosis. This is another tick borne disease that acts and looks EXACTLY like Lyme disease, but doesn't come up as a postive on a standard Lyme test. Your vet would have to perform a 4DX test....which is another "take a little blood and wait 10 minutes SNAP test"....only this one tests for Lyme, Anaplasma, Ehrlichiosis and Heartworm. I know some clinics only use the SNAP test for Lyme alone, and I can't help but think that's what your vet is using.
One of this problems is that a dog can have a silent infection for years before they become symptomatic...which means she could have gotten a tick on her any time in the last 4 years, it could have transfered the disease and it could have simply been dormant all this time.
I think the best thing to do is to have her tested for tick borne disease. In my opinion, one of the best (and fastest) options for that is the 4DX test. It only takes 3 drops of blood and 8 minutes for you to have a 'for sure' answer. You can read more about 4DX testing here: http://www.idexx.com/view/xhtml/en_us/smallanimal/inhouse/snap/4dx.jsf?SSOTOKEN=0
I did a little research on the CDC while I was waiting for your answers, and as it turns out, NY is right up there with us up here in MN as one of the states that has the highest instance of Anaplasmosis....so if your vet isn't checking for that...he should. You can read about it here: http://www.cdc.gov/anaplasmosis/stats/
I strongly suspect she's going to come up positive. Then it's just a few weeks (usually 21 days, actually) of Doxycycline, and she should be back to normal.
I hope this helps.