Sorry for the hard-to-understand dialog! This is just an advisory message that can occur after synchronization to let you know that your current view is out of date. In the future, we'd like to have synchronization proceed to refresh the view automatically when you finish your current edit, rather than interrupting you with that dialog.
For those who want to understand what's going on behind the scenes, here's a more detailed explanation:
The simplest synchronization case is where you change things on one device, synchronize those changes to the server, then synchronize them back to another device before making further edits there: in that case, OmniFocus can just apply those new changes to the database without reopening it, because OmniFocus knows there is no conflict between those changes and the local database.
Where things get more complicated is when you make some changes on one device, then make changes on another device before synchronizing them: those edits might be in conflict (one copy might check something off while another deletes it), so OmniFocus needs to reexamine all the transactions on both sides to make sure that it preserves whichever change was most recent. It currently does that by reopening the database, and that's when it displays that dialog.
The easiest way to avoid the reopen dialog is to synchronize as soon as you switch devices, before you start editing: the first set of edits would have been pushed to the server by the other device within one minute, so if you synchronize before you edit you'll be working with the latest set of data. But the reopen dialog isn't the end of the world, so don't worry too much about it!