Well, that seems more like a business strategy question than a technical one. You need to decide if you are still going to operate the companies separately or are going to merge one into the other. If you are going to operate under just one name and domain I would make a big marketing push to let everyone know that you are merging the companies into one and that this is our new business strategy and "Domain Name".
Then after some time has passed I would start redirecting all the content and traffic to the "NEW" site. with the standard 301 procedures. Making sure that everything you are keeping is redirected properly will help keep about 85% of the "Link Juice". There is always a little lost basically from how the algorithms work, but that is out of your control.