I'm not an expert, but if you have to refile, it seems like you would need to get w-2 forms from the company, and your 1099 would be void, if they have to relable you as w2, then they also would be responsible for all your payroll taxes, you really need to hire a lawyer ASAP that specializes in tax law, the company you worked for should be responsible for these issues, not you.
Never argue with idiots, they'll drag you down to their level and beat you with experience
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