What was the original flight time? If the change is significant you can probably get PAL to change you on an earlier flight if space is available. The problem with domestic flights is that they are usually the ones that get delayed when there is airport congestion in Manila. If the aircraft servicing your return arrives late because of a late departure from Manila and its a short turnaround then your flight will most likely be delayed. On top of that I once had been stuck in Cebu for an extra 30 minutes even if the plane was on time since they didn't get departure clearance from Manila due to air traffic congestion. If the total delays are more than 1 hour you might have a problem not being able to get to check-in your EK flight since I'm assuming they are booked on separate tickets.