Figure out?? The pilot is not figuring out anything, he's waiting for his  

That's why the company has POOL PILOTS.  The Pool Pilot position was created specifically for this dilemma.  The Pool Pilot is assigned to the vacancy, who gets travel to/from his domicile, accomodations, per diem.  The Pool Pilot also gets opportunities to do workovers.

The medical leave pilot must document his return is likely.  That can be as often as the company needs it to be to ensure the medical leave pilot is on a bona fide medical leave.   If he's still on company LTD, then it's very likely it is still a bona fide medical leave; otherwise, it would be an insturance fraud issue (a federal offense).

When it takes longer than 12 months for a pilot with a bona fide medical condition to get his medical back, then the answer to your last question is simple.   The CBA had it longer until the union GAVE IT AWAY down to 12 months, trading away your union rights for their benefits.

The compairson to 121, you are correct, we're not like 121, where you can go out on a medical LOA and return to the same place years later and fit right back in (because the 121 base/domicile has a large pool of pilots to fill their schedules).   The HAA 135 base pilot is can't come back if you give away his line to some other pilot while he is out sick.  That's why this is/ws a big important GIVE AWAY for the pilots in this industry!