Throw the pieces that came off away and do your rebuild. The early bikes didn't use them and most times during a rebuild they come off.
Lots of theories about why Honda used them but no one that I have ever heard of has every had issues when they were eliminated.
I know on my CM400T, they say it's to keep moisture from going down into the crankcase (something about running it or letting it cool down while on the side stand caused the right side to build up moisture). Ironically, when I did my top end rebuild, those 2 bolts were the only 2 bolts that had corrosion on them (rust)...
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