Question: I found myself in an interesting puzzle. Here is the simplified version:

I have a flight from A to C, connecting through B. I decide that from B I actually want to go to D, so I buy a separate ticket for that journey\*. The B-C and B-D flights are around the same time and with the same airline\*\*. Will there be a problem with checking in to B-D, given that at that point I will already be checked in on their system to the whole trip A-C, including the leg B-C? No luggage is involved.

Some extra information:
(\*) Every leg is relatively short within Europe, on economy fare. In particular, changing the A-C ticket to A-D would likely be pricier.
(\*\*) The B-D trip could be done with another airline. Does this change the answer?

Answer: 
**No**, there won't be any problem. Separate bookings are separate bookings and don't affect each other, even on the same airline.

I will note, however, that if you make a habit of buying A-B-C tickets and getting off at B, and give your frequent flyer number every time, the airline will eventually get grumpy. However, doing this once or twice is fine.
I would not count on being able to do this with the same airline. Many airlines implement [revenue protection](http://www.navitaire.com/Styles/Images/PDFs/New%20Skies%20Revenue%20Protection.pdf) systems that can automatically [cancel](https://thepointsguy.com/2017/08/illegal-book-2-flights-cancel-1) duplicate bookings. Since it's not physically possible to take all the flights you've booked, the airline may detect that and cancel one of your bookings. 

There may be a higher chance of success if you use different airlines.