I wouldn't worry about imported items. I would worry about patient data. You can't rename patient ID#s and everything is based on IDs.
I would think long and hard before I synced two databases with patients using the same ID#s. This is probably why he has not brought it up.
Now, when I reread your post, and if it is what it is, then your problem is simple.
First, it doesn't matter which, if any, has been updated. If you are using 5.0.28, who cares.
To find out which database you are using, just go to Amazing Utilities on any computer (or all if you want) and click on reset paths (it won't reset them if you just open that window). It will show you what database you are using.
There is no need to worry about which one you have been backing up. Who cares. Just back up the one you are currently connected to. You can back up the other database separately after. But, all you need is one good one. The one with patient data should be backed up, and that will be the one you are connected to.
As far as imported items, no big deal. Maybe a lot of work, though. You can do it manually. Just decide which database you are connected to, open the OTHER Amazing Charts folder, open the ImportItems folders and manually import those files. It will rename them for you.
When you find which database you are NOT using via the method above, go into the folder and either change the extension of the AmazingCharts.mdf database to AmazingCharts.old or move the .xml file out of the folder so it is IMPOSSIBLE to connect there.
I would be very careful about syncing, especially if there are any new patients.