| You do NOT start taking out the SS and Medicare taxes while you apply for the H-1B visa. You only do so when the H-1B visa IS APPROVED.
If your employer will not listen, get them to put the refusal in writing. When you get the H-1B visa, you can then file Form 843 and get the improperly-withheld SS and Medicare taxes refunded by the IRS. Your employer will NOT get his half of the taxes back, though, but he had his chance to listen to reason and refused, so he is paying for being stubborn.
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