Japanese Maples should not be pruned - they seem to make their own magic. But... stuff happens, branches break or get (messily) cut off. The good thing about living plants, even Bonsai, is that they are dynamic. Embrace this new turn in the life of your tree is a positive way.
The new growth will be a bunch of branchlets sprouting off the end of the cut branches - not a really attractive growth pattern.
I would be tempted to re-visualize this tree. Those branches will never be what they where so even it up. If you cut the pruned branches off at the main trunk and then cut the lowest one off the second main trunk on the opposite side, I think, in an asymmetrical way, it would be balanced again. If there is anything I could tell you about Japanese culture, it would be about asymmetrical balance.
Lots of little branchlets will sprout off anyplace you cut so be prepared to do some cleanup.