First, if the swelling is to one side of the throat and if it hurts, that's the lymph nodes of the neck. If a person gets an infection, say, in the gums, it will drain down into the lymphs, and they will swell up and hurt. A cold or nose infection will do the same thing. It will subside on its own.
Acid reflux is within the throat and thus normally will not affect the thyroid gland, which is situated outside the throat. Reflux will sometimes cause erosion of the tissues inside the throat, but not a lump near the outside of the throat.
If I understood your post correctly, if you do have nodules on your thyroid, and now you have this a rather larger lump near there, then you must visit an endocrinologist so he can check out your thyroid gland and see if the lump is somehow connected to it, like if one of the nodules has gotten too large. Your physician can refer you to the specialist for that.
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