An Eljer Savoy, going by the number inside the tank. 1.6g but has a 3.5g Korky flapper on it.

It does flush, with the sucking sound at the end of the flush after the bowl is emptied, but the flush itself is lazy. Is that the best it is ever going to be, seeing that it does not have a siphon jet? Eljer calls it Siphon Vortex.

Does having the 3.5g flapper instead of the 1.6g flapper hurt the flush?

Wasting water is the downside. You should always get the flapper designed for the toilet or you are borrowing trouble.

No disputing the wasted water. My question was a different one though. "Does it HURT the flush?"

In other words, would a 3.5g flapper lead to clogs that a 1.6g flapper might have avoided?

i wouldn't think it would hurt the flush
sometimes too much water results in a double flush but if yours is not doing this then it is OK.
the height of the water in the tank will, obviously, affect the flush.

It wont hurt the flush, but if the toilet clogs, the extra water will make the toilet overflow. You want the flapper to close at the moment the water evacuates the bowl. Most 1.6 flappers have an adjustable float above the flapper. You adjust the float until the flapper closes just as the bowl emptys.