On any platform, the application storage directory is in a "Local Store" subdirectory of a directory that is named based on the application ID and publisher ID. And the parent directory of that directory (the appID.publisherID directory) contains all other application storage directories.
So, if you know the publisher ID, you should be able to find its application storage directory this way (in the new application):
var rootAppStorage = new air.File(air.File.applicationStorageDirectory.nativePath).parent.parent;
var oldAppStorageDir = rootAppStorage.resolvePath(appID + "." + oldPubID);
Note that calling new air.File(air.File.applicationStorageDirectory.nativePath) creates a File object that uses the file URL scheme (not the app-storage URL scheme). (You probably got an error if you tried to access the parent directory of air.File.applicationStorageDirectory directly. AIR will not let you navigate to the parent of the application storage directory if the File object uses the app-storage URL scheme.)
Thanks for the reply, that probably would have work great. Instead I just setup an array that stored the path each operating system uses added that to user.Directory and then checked to see if it existed and if it did used copyTo to get the sqlite database.