Upvote:5
While nothing prevents you from checking in for both flights, there are several potential issues:
When you cross security, you have to show a boarding pass. On some airports the guard marks it and on other it gets scanned. In any case, only one of your boarding pass would have been seen by security.
If you are on an international flight, you also have to perform exit immigration and they sometimes scan the boarding pass or place a sticker on it to show that you went through the process.
Gate agents when you board the plane do not always look at all the markings but your boarding pass will definitely stand out if it's the only one with stickers or marks. They also scan the boarding pass which is another way they could notice that you did not go through the process (less likely but not impossible, it depends how connected the airline and airport systems are).
Most importantly, if you are checked in, the airline expects you to be on the airport on your way to your flight, so they will issue multiple calls and this may delay the flight.
What would be safer is to wait for the last minute to check-in. You can use a flight tracker to see if the plane has landed from its incoming flight and have a pretty good if it will be late. There is no guarantee though, since even if you depart from the traditionally reliable flight on-time, the plane may return or land in an unexpected location due to technical issues, staffing issues or weather (all these have happened to me multiple times) or even an unruly passenger (known to happen but not experienced that yet).
Once you know which place is already at the airport, that will be your best bet to check into and not checking to the other flight will be less trouble than checking-in and not showing up.