AndyM got there first
In medical terms, I would seek another opinion. Mobile towbar fitters deal with a wide range of vehicles and are generally pretty good with this sort of thing as they fit SCRs on most of the towbars they fit. You can generally arrange a convenient place to you both to have it checked out.
If you have an amp meter, then change it to volts, and then put it across the van's main battery with the engine running. It should show something up in the 13.8 to 14.4v range.
12.4 volts indicates a flat battery.
Your SCR appears to be working as running the engine restored the pump's flow and allowed you to get on with the job. If the SCR fitted is of the
intelligent type then it is set so it only kicks in to charge the second battery once the van's starter battery has been charged. It takes about 15 sec to several minutes on our vans before you hear the solenoid kick on as the van's battery has priority. If he is testing your second battery during this initial period then it won't register as being charged.
I would 'bench' charge your 44 amp battery and find a garage that can do a load test on it to determine if the battery is faulty or not.
I'm also going to stick my neck out here and add that I believe that a 44 amp battery is too small for the daily requirements of a single WFP operator. We wouldn't go below an 85 amph leisure battery.
If your pump is drawing 6 amps an hour (which it can do) then 4 hours work has already drained the battery to half of it's charge. If the battery isn't fully recharged by the time you start work the next day, then that battery will just get flatter. If you start with a full glass of water but you keep taking more out of it than you put back in, then you will eventually empty the glass.
A starter battery isn't designed for this sort of 'abuse'.