On these modern bikes, the battery is an essential component of the electrical system! Disconnecting the battery, while the bike is running, is akin to breaking the electrical circuit. The bike will stall out.
I have, unfortunately, had significant experience with the charging system on Orion, last year... All due to my negligence.
I had to replace my stator, VCR (Voltage Control and Regulator), battery, and VCR wiring harness.
Long story short, I reassembled my generator, sloppily, and got one of the dowel pins wedged between the stator and rotor. It did catastrophic, significant damage to the stator, the regulator, and of course the battery. The rotor was not damaged! That is one badass piece of metal!!
Everything Ray says, is 110% spot on!!
One day, after I get over my embarrassment, I will document what I effed up, and how I fixed it.
On these bikes, a GOOD battery makes all the difference!! It cannot be stated enough on these threads.... Just because a battery shows "good" voltage, doesn't necessarily mean is it a good battery! It HAS to have the Amps to push a good voltage or it is a dead stick, period! A neglected battery will cause ALL kinds of seemingly "electrical problems." When in fact, it is just a bad battery.
IN general, if you don't eff something up, while reassembling, the charging system on these bikes is robust and essentially bulletproof! The only "weakness" if I can even call it that, is the battery. But that is Not an FJR problem, that is a modern bike problem.
The battery is an essential, integral component of the electrical system. If it is not in top condition, the electrical system is compromised.
I am just offering my opinion. YMMV...