Mike -- if it's an '05, then the OP's "AE" designation is incorrect, since all '05's have clutches. His info shows it to be an '05 with ABS, which makes it an FJR1300A.
I'm thinking that it's probably a good thing the dealer still has it and is willing to address the issue. They likely have the tranny apart (noting 9 hour estimate).
Not gonna do a search, but this has gotta be caused by damaged dogs or bent internal shift forks, doesn't it? And if so, it's more likely than not caused by previous owner hammering on the shift lever at the wrong time under the wrong conditions. Either way, once fixed, I wouldn't expect a problem later -- if the dealer has the tranny open, they're likely gonna make right whatever they find there.
Would they XSB? I wonder who's footing the bill for this repair. If it's the dealership, they may take a "good enuf" approach and cut costs by not replacing each and every item not found to be within spec. Indeed, they might night even run it completely to ground.
Or is it still under warranty? If so and the problem persists, it will only come back so maybe they'll do the right thing and fix it the way we would if it were our personal bike and we didn't want a recurrence. Not real sure about this one...I'd need more info before I would simply take the dealer's position as the final say.
They will definitely need to open the tranny just to see what's going on. I would want to see and understand the HW and their intended fix before consummating this one.
Just sayin'.
W2