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I'm not 100% sure of your question, but I think what are you asking is if it is permissible for an employer to not pay full pay for days when partially worked, even for a salaried employee.
Typically, the answer would be no. An employer can't prorate the daily pay of an salaried exempt employee if they work any hours during that day. So, if you worked 5 hours in a day, under normal circumstances you'd have to be paid the full day (though they could deduct hours from vacation).
However, FMLA is a special exemption to the salaried exempt rule. It has it directly in the FMLA statute. You can see that here at 29 CFR 828.206 which discusses the interaction between FMLA and the Fair Labor Standards Act (FLSA) that creates the "salaried exempt" concept.
Section (a) clearly states "If an employee is otherwise exempt from minimum wage and overtime requirements of the FLSA as a salaried [employee], providing unpaid FMLA-qualifying leave to such an employee will not cause the employee to lose the FSLA exemption. This means that under regulations currently in effect, where an employee meets the specified duties test, is paid on a salary basis, and is paid a salary of at least the amount specified in the regulations, the employer may make deductions from the employee's salary for any hours taken as intermittent or reduced FMLA leave within a workweek, without affecting the exempt status of the employee. "
So, on that basis, the employer could absolutely allow a salaried exempt employee to work from home for 5 hours a day, and pay that employee a prorated payment based on that partial day's work, with the remainder being covered by FMLA leave.
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