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They thought she had a pyometra in her neck?Does the swelling seem soft and squishy, or is it hard?Did the vet do any blood work?
Any vomiting or diarrhea?
Thanks for answering my questions.
Without being able to see her personally, I suspect that she's got something called 'localized edema' in that area. Localized edema in a singular area can be the result of injury, burns, obstructions in an artery due to something like a blood clot or even cardiac issues. The fact that you can essentially rub the swelling away makes me wonder if the lymph glands in that area are swollen with fluid that the heart isn't able to get rid of due to compromised function.
When it comes to your next step, my suggestion is that you have a FNA (fine needle aspirate) done to test the fluid in the area. This involves taking a needle and syringe and drawing off some of the fluid in the lump and then looking at it under the microscope. Hopefully this will tell your vets (and you!) what is going on in that area. If no diagnosis can be made this way, then a biopsy is your next step. This is where they remove a bit of the tissue in that area and send it off to a lab for evaluation. They also suggested x-rays and perhaps a full cardiac work up to make sure it's not the heart that is causing this problem.
I hope this helps!!