The title pretty much says it.
If you assign a bonus that drops your rep back below 50, you can't comment on anything (popup appears: "You need 50 rep to comment"). A nice reward for setting a large bonus.
I haven't tried to do anything else.
Perhaps the "rep" threshold for comments (and other actions?) should be "current rep plus sum of bonuses awarded"? This would probably apply to SO and other StackExchange sites, too.