FMLA in a Resignation Period

This just must be my month for strange FMLA brew!!

We have a company that was in the middle of a reorganization and had instructed a manager that they were adding duties to her position. The employee made it known that she did not want to perform these new duties and verbally resigned. She was told that we would accept her resignation, but in order to leave the company in good standing AND to be eligible to receive her unused earned PTO she would need to work the notice out (30days) AND perform the new duties through the final date of employment. This was on a Friday.

The employee comes in the following Monday morning with a doctors notes stating that she was going to need to be off work for TWO weeks for high blood pressure and other health conditions. She was given FMLA paperwork and subsequently approved as it was noted as a serious health condition...(and also gave the employee a way to get paid their PTO, as typically any absence during the resignation period would result in forfeiture of PTO, but FMLA is a protected absence so PTO is being honored).

Meanwhile, the employer wants to know if they can recruit for the position that is being vacated. We said absolutely, because she gave verbal resignation and a date of final employment (although we prefer it in writing and told the employee this). The employer asked what do we do when the employee comes back after two weeks. We told them that the employee would need to continue to perform the restructed tasks through her final date of employment OR failure to do so would mean not complying with a condition of employment and she would be self-terminating early.

Yesterday, at the end of the TWO week period, the employee comes back with another doctors note, extending her absence by another TWO weeks. The employer wants to know what happens when the FINAL date of employment (per the resignation) comes up before the end of this TWO week extension. My thoughts are that the resignation and final date of employment still stand and FMLA would end on that day, and she is no longer employed.

Any thoughts to contradict that action? Thank you for the feedback!!