What could cause the headlights to blink after replacing the alternator?

Hey Melinda==Check to make sure there is a good ground between the engine and body with no paint or dirt. Also remove both battery cables and clean both ends. This should do it. GoodluckJoe

Maybe a loose wire or a bad connection to the headlight itself.

There may also be a security function that has been triggered by the battery being unhooked during the alternator installation. My Jeep does this every time the battery is reinstalled in the circuit or is drained and recharged. I must then reset the security to get it to function properly. Good Luck finding the problem & hope this was helpful, Joe.