Kind of rare to have a PTO clutch problem on any of the BX series. I can't recall the last time I was into one other than for an axle seal here and there, and IIRC an axle bearing that had baling wire wrapped up into the seal and bearing destroying both.
If you engage pto and then move your pto selector lever does it make any grinding noises or anything? I'm leaning toward a pto range/selector linkage problem more than anything.
I don't remember any shear bolt in the PTO system and shafts, other than your implement(s) themselves.
Any warranty left on it? Can you get a 2nd opinion from a different dealer?
If it were at my shop, the first thing I'd do would be to pull the screen out of the bottom of the transmission and inspect it. If there's a bunch of metal on it, chances are a shaft or gear broke, something along those lines. If a bunch of clutch "mud", the PTO clutch itself is likely suspect, but again, as long as I can remember (which was back way before the BX's even were introduced), I can't recall having to go into any of them other than for one HST failure and a few seals and bearings.