OK,
The completely safe, solid, by-the-book answer is that you will need to either:
1) Strip the motor and replace that casing. Good news here is plenty of R6 motors have suffered gearbox or other mechanical failures, and you only need a good top casing, so the donor part shouldn't be too expensive. You will, however, need time and rather a lot of gaskets...
2) Swap the motor out for a good 2nd hand one. Most motors bought from a breakers will have something like a 28 day warranty, so you want to be in a position to swap the motor out very soon after purchase to give you time to find any issues. This can be expensive, but it's the fastest fix compared top option 1.
However, you've got the bits that came off, and there's a fair bit of surface area there to work with, as well as a bolt to hold it in place. Do the bits fit neatly back on to fill the hole?
I would talk to someone who knows about these things (such as a local engineering firm) to see if there is a possibility to attach this back in place using something like JB Weld, or actually welding the piece back in. With that bearing so close, you'll want to be very careful about anything getting in there that could damage it though. Practical Sportsbike magazine actually had a piece on repairing crank cases like this this month or the one before, albeit for non load-bearing parts which I'd say that is.
Definitely worth investigating repair options at this stage.
Jambo
Edit: Also, see if there's a tab washer to go behind the nut, and buy one if so
