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This situation appears to be illegal since if you are treated as an employee, you should typically be paid all of your earnings in wages and not through a 1099 which indicates you are an independent contractor.
To resolve this, it is normally best to file a complaint with the labor board to investigate and have you properly classified. Here is a link to their website:
If the employer has at least 50 employees, you would typically be entitled to protected leave under state and federal law if you are properly classified as an employee and have worked for the employer at least 1,250 hours in the last calendar year.
If the employer is not willing to recognize your right to receive such leave, then it is typically best to retain a local employment law attorney to aid in enforcing your right to leave.
Good luck and take care.
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