When the mobile file is updated, the previous version will be overwritten, so none of that data will be preserved. That's why you want to edit the "Zync - Is a new version permitted" script in your mobile file to check for unsynced changes in the tables you specify before the new file is installed. We have some notes about that in the "Is a new version permitted?" section here:
http://www.seedcode.com/pmwiki/index.ph ... obileFilesYou could distribute the new mobile file prepopulated with any data that will be shared among all users (price lists, etc.), but any data that is filtered for each user will have to be downloaded on the first sync.