I had this exact issue earlier this week, and called Southwest for help. Here's what to do:
1. Log into your rapid rewards account on southwest.com
2. Click on the My Travel link on the right hand side.
3. Click on the trip with the lower point tickets
4. On the upper right of the confirmation, in blue type it says Change. Click that. You'll be changing to the SAME flight - so don't worry about losing your seat.
5. Select the flight to change (you need to check the box on the left of the screen). Hit continue
6. Click on Select New Flight (assuming you want to be on the same flight/day, if not change it on this screen first).
7. Select the flight you and and continue clicking to confirm the change.
Basically you will be changing your flight to the SAME flight, just using fewer points. The extra points will be credited back to your account for later use.
Hope that works for you!