Not sure what you are encountering here as it’s not possible to create databases in DEVONthink to Go, nor is it possible to import a database from an iPhone to a Mac before syncing. It other words, the database cannot possibly be only ‘on the iPhone’ unless it had previously been deleted from the Mac where it originated. It might be helpful if you could provide more details on how you have DEVONthink configured on your Mac and iPhone, and the steps you took leading up to this.
If you sync a database to DTTG, and then close the database on the desktop, you will see the database in the DTTG sidebar but you wil not see it listed in the Synchronize panel in DTTG. I suppose, then, you could conclude the database is “missing” or “deleted” on the desktop. In fact, it might be deleted or it might merely be closed.
Precisely how did you try to import your database from your iPhone to your Mac?
Another question-was your iPhone originally synced to DEVONthink on this Mac? DEVONthink to Go can only be paired to one Mac-you cannot use it to sync databases from one Mac to another Mac.
Edited to add, if you did sync DEVONthink to Go on your iPhone to DEVONthink on a different Mac, then yes everything on the iPhone will be replaced by what you are syncing from the different Mac (Inbox, recents, database(s), etc.).
But it had to re-install Mavericks after the Yosemite-misadventure. So, for DTGG it might look like a new Mac. (By the way, there is iOS 81.3 on my iPhone 5).
I synced by tapping the two arrows in the middle of the bottom bar of the home screen in DTTG. After that I selected my Mac from the list. I selected the databases that I wanted to be synced and that was it.
This may be totally unrelated, but as I am curious-how did you attempt to import from the iPhone to the Mac?
On the sync, if I understand correctly you had a database (let’s give it a name-CDs database) named CDs database on both the Mac and the iPhone. You attempted to sync the database (and three others) and now the database is missing from both the iPhone and the Mac?
It was deleted because DEVONthink treated your iPhone as a new sync device to the database, due to your reinstall of OS X. Technically, your other 3 databases and the Inbox were overwritten on the iPhone as well-they did not ‘sync’ any changes/new documents from the iPhone back to your Mac.
Do you have a backup (Time Machine, etc.) of CDS database that you can restore to your Mac? If not, the only other option I can think of would be to restore the iPhone from an older backup and use DEVONthink to Go’s ‘Export to iTunes’ function to recover the documents. Not something that I would like to do!