Syncing two databases in a redundant network architecture
That's tough. Even 5 minutes of downtime for a reboot would put you in a situation with out of sync data. I really think you should look into other options.

I'd definitely recommend mirroring here instead of what the app is doing. With Synchronous Database Mirroring with a witness, the two databases will be in sync and you'll even get automatic failovers. It's not hard to setup either. 

You could use Transaction Replication as it can handle a server being down and pickup where it left off. But I don't consider it to be an HA or DR technology. Mirroring, Log Shipping and Availability Groups are the HADR technologies. Specifically Sync mirroring and Sync AG are HA, async mirroring, LS and async AG would be DR.