Employment Law Questions? Ask an Employment Lawyer.
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You have to present evidence of the fact the leave was covered under your FMLA and tell them that if they continue to try to punish you over this you will file a complaint for harassment and retaliation under FMLA with the US Department of Labor and will seek damages against them for the harassment and retaliation.
If they will not accept your proof, then you need to file your complaint to the US DOL and most times they will resolve the issue with the employer.