Ah, that's a shame.
I managed to put a hairline fracture in one side panel before I managed to shave one of the pegs properly. It's barely noticeable, and that's not the problem, it's now weaker on that part. I also can't put the clips in. They just won't fit.
A suggestion: Take the parts, trace them onto some thin MDF, cut it out and sand it down to fit better.
Someone on the forums also made a lego case.
I did make a 3D printed case, but I haven't test printed it yet. I'll be buying a much larger 3D printer in the next few weeks / month or so and want to do the design again, and try to print a case.
Good luck and keep us apprised of how to get on.