Don't tell me that something was consuming his arm on the process and they decided to cut it off? You're planning to use dark magic or glyphs to cut the connection between Jonathan and the whip?
Important of note, before anything: This is NOT set in stone yet. I'm telling you guys all this, but in the last second everything can change.
Maybe a glyph will be involved. For a myriad of reasons that will explain more than one question at once. This specific bit about Jonathan's severed limb is the perfect setup to explain how the Belmonts were cured through a glyph.
So, it's not like it was "consuming his arm" but more like the life drainage effect was consuming his entire body. VEEEEERY slowly, much slower than it consumed John. But it was certain that Jonathan would end his days bedridden thanks to this.
At a certain point, the sisters along with Charlotte found a way to restore Jonathan's health by isolating the life draining effect in one limb, and taking it off. Jonathan agreed as he couldn't take being incapacitated.
This life draining effect is nothing more than a memory of Richter living inside the body of the wielder. A parasite memory, if you will. The more one wields the whip, the more life force this parasite memory requires. Jonathan did not wield it enough for the memory to consume him, but he did it enough for it to linger inside his body and cause his health to decline slowly. Once he got it off, he was back to top condition.
So, I wasn't thinking precisely "an arm". I don't have this decided yet. But, whatever limb it is, it is replaced by a construct powered by magic. If it's a leg, for instance, it is replaced by metal/wooden/whatever leg that moves through a spell cast by Charlotte, which could be a glyph using Jonathan's own life force to move the limb.