I have two APM 2.5. I have been busy the last year or so and just getting back in.
The only difference between the two APMs is the 2.6 does not have the GPS and compass?
I was thinking about severing the connection on the 2.5 and adding the HMC5883L for better performance.
Welcome back. Yes, that's pretty much the only difference (that I know of) between the APM2.5 and 2.6. There's a video on this wiki page showing how to cut the trace to disable the onboard compass.
Nope - just upgrade to the latest firmware and update Mission Planner too. I just cut the trace on my second APM2.5 and all works better than before.
Viewing Randy's video on how to disable the compass is a must. I used a small box cutter and pushed the sharp end through the trace in about 6 pushing scrapes while looking with really good lighting and the strongest readers I have. Use a VOM to confirm trace is cut. Careful of the surface mount part nearby that stands fairly tall.
did everything according to the instructions and started getting the error: bad compass health
how to diagnose resolve this problem?
That doesn't sound good. I think that could be a hardware problem. You can check in the mission planner's flight data screen's status tab at the bottom and see if mx, my and mz are returning values. If they're all zero then I suspect the compass is toast.
I'm guessing that your APM is thinking that a compass is connected but it really isn't. This is just a wild guess with not enough information to go on from you. I'm assuming you have cut the trace and tried connecting an external compass from an earlier post. I would recommend a 3DR compass/GPS module which I have used on two conversions and both went very well following Randy's instructions.
I got the same "bad compass health" message on my first conversion and found that the smaller compass plug was not all the way seated on the GPS/Compass module. Look at the plugs with some magnifying help and re-seat. The one I had a problem with was the I2C? cable on the GPS/Compass module side.
To make things even more confusing, the compass appears to work on the HUD display but in reality it is not working only the acc sensors are making it appear to work.