Update: the official word is to use the same bundle ID. See here.
I did a little more research and it turns out that if the version number for the Mac App Store is newer than any version number of any apps with the same bundle ID, the App Store will let you buy and update it. So all I have to do is submit a new version of Sound Studio to the MAS, and people will be able to buy it.
And for the future, I’ll need to update my trial and upgrade version of Sound Studio to use a new, unique bundle ID, so that this problem doesn’t happen again.
I’m thinking that Apple won’t do anything other than remind developers to choose a unique bundle ID that is different between the MAS and outside-the-MAS versions of the same app.
I’ve had a few support emails asking about a discount for upgrading from a previous version. Sorry, but the Mac App Store doesn’t allow for that, so you’ll have to either buy for the regular price in the MAS, or buy it through my web site.