Filling in baffle holes

The fella I bought the bike from drilled 3 half inch holes in the baffles to make the bike louder. Loud is not really my style. Any ideas on how to fill in the holes? 
2000 vs800

It's not clear to me from your message exactly what you've got but people do this either by drilling through the baffles with a long drill bit or by driving a spike through them. I had the latter situation on the VX800 I bought and i considered filling the holes by knocking a steel bar or screwing a piece of threaded bar of a slightly larger diameter into the holes. Would this be feasible in your case. There would be a slight reduction in volume of the compartments but the original path would be restored.

You can buy universal baffles and the padding to go with them if you want very cheaply from Ebay. I forget what size you need but just measure the opening with a tape. Cut the old baffle out with a plasma cutter if you have access to one, or something like a Dremel cutting wheel if not. You only have to drill a single hole for the locating bolt to hold the new one in.