Many members report feeling worse when they first start on a thyroid medication because it takes time for their body to get used to having hormones it's been doing without. Others can have reaction to the fillers/binders in the pills and simply switching to different manufacturer is sufficient.
It sounds like your endo is trying to get a "baseline" test panel done, which would be done after all the med is out of your system. Because levothyroxine has a long 1/2 life, it will take a while to get it all out of your system, which is probably why your endo is waiting 5 weeks to retest.
Yes, you will most likely have to go back on the medication at some point.
In addition to the TSH test, you also need to have the Free T4 (FT4) and also a Free T3 (FT3). FT3 and FT4 are the actual thyroid hormones and correlate best with symptoms, especially the FT3, which is the active hormone. TSH is a pituitary hormone, that stimulates the thyroid to produce hormones.
Hopefully, your doctor will also run antibody tests to determine whether or not you have Hashimoto's Thyroiditis, which is an autoimmune disease in which the body sees the thyroid as foreign and produces antibodies to destroy it. If he doesn't run these tests, you should ask for them. They are Thyroid Peroxidase Antibodies (TPOab) and Thyroglobulin Antibodies (TGab). Hashimotot's is the number one cause of hypothyroidism in the developed world.
When you get new blood work done, please post the results and reference ranges, and members can help assess the testing/treatment.
sorry, the ref range of my T4 free is 0.76-1.79 ng/dL