My advice would be to
- keep the ports, because you'll need them to build a shipbuilder and then ships to protect your islands from invasion
- build a few units and split them into stacks of single units, take them all outside the fort/keep
- make sure the provinces have a high level of happiness, so that if they are invaded, it will be more likely to generate loyalist rebellions for you
- if you have spies, place one on each island, so that if they are invaded the spy can stir up a loyalist rebellion
- build ships anywhere as fast as you can, make a line to your islands and move heirs there to command the armies, as they can't be bribed
- if you happen to lose one island or two, keep building up your navy, take over the seas around the islands and invade them back; losing one or two provinces is not a gamebreaker for the Byzantines in my opinion, as long as you can hold on to Constantinople, Greece and Nicaea (the richest provinces)
If the Eggies have ships around Cyprus or Rhodes, it means they can possibly reach your mainland, which is much more important to defend to keep your empire intact. I'd focus on defeating their navy and take it from there.
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