I don't have a granite counter top and so I have no experience with them. So, maybe go down to any place that makes granite counter tops and buy a piece of scrap unsealed granite off them for $5 to use as a test piece.
Check that nail polish remover doesn't harm your granite. It shouldn't.
Try using nail polish remover to remove the sealer where it's flaking off. If it removes the sealer, then you can use acetone to remove it, which you should be able to buy for about $20 per gallon at any paint & hardware store or home center.
Go to the cleaning aisle of your home center and see if you can find a phosphoric acid based toilet bowl cleaner. You also should be able to buy phosphoric acid based toilet bowl cleaners at any place listed under "Janitorial Equipment & Supplies" in your yellow pages phone book.
Check that the phosphoric acid based toilet bowl cleaner doesn't harm granite.
Phosphoric acid is the active ingredient in most bathroom cleaners because it cuts through soap scum like a hot knife through butter, but won't attack chrome, even in strong concentrations.
You can use a phosphoric acid toilet bowl cleaner to clean up soap scum without having to worry that it will damage the chrome plating on your kitchen faucet or your stainless steel sink.
The only thing that I know of that cuts through soap scum better than phosphoric acid is oven cleaner. Check that oven cleaner doesn't harm your test piece of granite.
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