Jakobox-
I'm really sorry for the trouble this is causing! I'm guessing at least part of what you're seeing is indeed caused when the same item is edited on more than one device.
For performance reasons - the iPhone is an amazing device, but it's still about a thousand times slower than a low-end desktop machine - conflicting edits to the same item are resolved on a per-item basis, not a per-field basis. (Doing the latter would cause syncs to take much, much longer than folks have told us they want to wait.)
What does this mean? If you sync two devices, then edit an action on both machines - change the note on one machine and the start date on the other - and then sync both machines again, you're not going to see each machine get the change from the other machine. You're going to see one or the other change win out over the other - specifically, you're going to see the change that happened most recently win out over the earlier one.
However, what you saw happen here doesn't quite match what I'm describing here. The 40 inbox items, for example, couldn't have been edited on both devices.
Just to be sure they're gone, on your Mac, can you please bring up the "All Items" perspective, then use the toolbar search field to look for them by name? My hope here is that the items were re-filed but not actually removed from the database.
If that doesn't turn out to be the case, please contact the
support ninjas so we can look at your sync database and see if we can determine what's going on.