I have Hashimoto's and have had hives for 16 years and never knew what caused them. They seem to be somewhat hormonal--or at least get worse at different times of the month. I was diagnosed about 2 1/2 months ago with hypothyroid and TPO antibodies. My doctor has me on 50 mcg synthroid and my TSH has come down to 1.5 (from between 4.83-5.05), while my antibodies are now at 133 (from 149 when I started meds)--that was my 6 week reading. My doctor said the TPO antibodies will come down slowly with the synthroid--although I'm not sure how long it will take. I have a friend who went through something very similar as well and she was "back to normal" at about 6 months. I hope the hives decrease as the TPO level goes down. Good luck!
Have you considered that you might be allergic to something in either the Armour or the Allegra? Fillers in drugs often cause people side effects. Also, if you've been hypo recently, and the long, cold, dry winter has just ended, could it be a secondary skin problem that hasn't been able to heal?
I've never heard of antibodies causing any symptoms (doesn't mean they can't), except, of course, destruction of the thyroid.
None of the hypothyroid meds (Synthroid, Levoxyl, generic levothyroxine, Armour, etc.) lower antibodies. Once your antibodies are elevated, they remain that way and keep up their destruction of your thyroid. This can take many years. There is no way to lower antibodies. The only thing I hear consistently recommended is selenium. However, there have been no large-scale studies proving selenium is effective, either...doesn't mean it isn't, just hasn't been studied.
So, I think you should try to get to the bottom of your hives problem by investigating the side effects of the meds you are taking or see your doctor about other possibilities. If you wait for the antibodies to go away, you'll be suffering for a long time.
I used to get a lot of hives. I am also on Armour 150mg. How long have you been on the Armour. I think sometimes it takes your body some time to get the antibodies to come down. I haven't had much itching anymore. I would think with the allegra you would get some type of relief. My antibodies for 1,000 when I was orginally diagnosed. I don't know what they are now but my tsh is .00 which I have been feeling fine on that. I have heard of people on Armour getting this reaction if it keeps up you might consider switching to a different thryoid med but give it a little while.