There really isn't an easy way. Unless there is a 3rd party product, the only way that I can think of doing that is to export the items (images won't be exported or combinations for that matter) and import them into a single shop. You can also copy products to another shop and move them to another category. I did a similar operation when I crashed my site by trying to modify the MySQL backend. I ended up working very, very late on that project. Needless to say, I'm not doing that again!
You can also try to manipulate the MySQL backend, but I wouldn't recommend that unless you really, really, know the database structure. Either way, I would make a backup of the site and DB, and play around with it locally before making any changes to the production site.
You can use XAMPP to run a site on your local machine (or some other PHP, Apache, and MySQL product) This is what I do now.
What might be a good idea is to export products from the production site, and try to import them to your local test site. Then you can see what will happen and what you have to do.