Thank you for the additional information and I appreciate your patience in trying to help me understand what you are seeing.
It is a good thing that you do not see any broken wires, but we have to remember that we could have an internal break that isn't visible. What I would like you to do is check for the presence of voltage at the connector you mentioned under the seat. I believe you are saying that is the factory Honda wiring harness at that point and it is where it is connected to the harness for the accessory lights on the saddlebag. Typically there is only one feed wire for the brake lights, so if you have brake lights on either side, that should indicate that the factory wiring is not the problem.
You mentioned "spliced in". If it was spliced in with the 3M connectors, which are the connectors that clamp over the one power wire and then the new accessory slides into the connector half way and it has a sort of M shaped metal tab that is squeezed down cutting through both insulations and making the connection. The sad reality is these are not great long term electrical connections.
What I would like you to do next, since you have already successfully completed a visual inspection of the wiring, is to start checking for voltage on the wires. Usually when checking, you start by checking for the voltage at each connector. In your case I would like to see you start at that connector you mentioned under the seat where the factory harness connects to the accessory harness. Providing you have power there, work your way towards the socket checking at each connector you come to until you end up checking inside the socket itself on the contacts for the light bulb.
If you have any questions, let me know. Hopefully I was able to explain that without confusing you even worse. Let me know what you find and what additional help you need.