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.
1. It's unlikely but not impossible that you will get problems at check in. This can be interpreted as you cancelling the "B-C" leg, which incurs a change fee (as stated in the contract of carriage). It sounds insane, but airlines want you to pay for not taking a flight that you have already paid for. They can enforce this if they detect it
2. You need enough time. Depending on the airport and airline, you may have to leave the secure area, check in, and then go through security again. In many cases check in closes 1 hour before departure, which may be more than your connection time.
3. Any return flights from C to A would get cancelled by the airline.