I have a 353 with a pair of 525's and have removed the ST box. I installed external rubber flappers on the exhaust tips 2 years ago. I noticed at the end of this season that on one exhaust tip, the internal flapper is chipped off and it appears it is cracked where it attaches to the exhaust pipe. Two questions here:
1. Are both internal and external flappers necessary?
2. is there an easy way to replace the internal flapper or should I even mess with it?

If it's the standard 4" thru-hull exhaust fitting, the internal flapper is Merc part #12647. You can drill out the rivets from the bilge side and the replacement part will have bolts and nuts. Just Google the part number and you can get decent pricing.

X2...

I would highly recommend an internal and external flapper especially if you have since removed the silent thunder.

Why cut corners on inexpensive parts to protect water ingestion on your motor, which will cost big money to fixshould it happen.

i.e. my friend purchased a cobalt 2 years ago, had water ingestion due to corrosion on 496's. The piston rods bent so bad that he had to replace the entire block. Boat hasnt been running right since the change.

I would keep both. I even hit the captains call when reversing just for another added layer of protection from ingestion. Especially now with the ST box off. Last thing I want to be doing during the season is breaking down the block to replace a bent rod.