Reimbursement for the rental car seems like YMMV, but almost certainly they'll give you some sort of refund for the PHL-LGA segment. In some cases the refund for a leg like this is a joke amount (it's not proportional to distance or anything like that so it could be $20). But I had a similar case not that long back where I had purchased someone's flight DFW-LGA-DCA (with a daylong stopover in LGA, to do work). LGA-DCA ended up getting canceled for weather, so he took the train and I put in for a refund and was pleasantly surprised to get $80 or $90 back on a $200ish ticket. That x multiple pax could be greater than the cost of your rental car, and I imagine there's no harm in putting in for the refund.