My cover has small holes and has slowly been sinking. Rather than replace/fix the cover, for now I'd like to siphon the water on the cover back into the pool (under the cover). I have an electric pump that is used for removing water from the cover. Can I run my output hose back into the skimmer and into the pool water? Can a siphon be created if the outlet is submerged in a body of water? Any help is appreciated. Thanks.

You won't get a siphon to work since you are going from the same body of water as you want the water to flow to.

Sorry to say it but, you can pump the water back under the cover to try to stay ahead of the leaks, but you can't siphon it. The trouble is that it's the same body of water - a siphon requires separate bodies of water and a difference in height.