Short answer: No. Even when the employer is allowed to recover premiums it paid during FMLA leave, COBRA cannot be conditioned on that repayment.
The IRS COBRA regulation is direct: the right to COBRA continuation coverage cannot be conditioned upon the employee reimbursing the employer for premiums it paid to keep group health coverage in place during FMLA leave. That holds even when the Department of Labor rules permit the employer to recover those premiums.
Treat the two separately: send the COBRA election notice on time (the qualifying event is the last day of FMLA leave), and pursue any premium recovery as a debt, through lawful payroll deductions or collection.