1. Have you been paying for the LTD coverage for them while they are on leave? If so, they would likely be covered. In fact they could have been collecting LTD during the FMLA period if they otherwise qualified. I do not believe it was necessary for you to cover LTD, only the group health insurance.

2. Any time they were qualified (usually after they had been disabled for 90 days). You should consult your LTD plan provider as to the details.

3. None as far as I know, though I would lend any assistance you would give to any other employer seeking to file a LTD claim.

4. A waiting period for what?

5. Applying for claims on a policy you already have isn't a preexisting condition. That applies to people who incur some condition and then go buy insurance in order to treat it.

6. THe best suggestion is to not treat the FMLA employee any differently than you would an employee that was actively working or just on some other form of leave.