One of the main reasons we decided to start over is that we were afraid we had water issues because the deck was never properly flashed. This was definitely confirmed by the state of the sheeting under the ledger boards on our bays. The ledger just fell off because the sheeting was so rotted. Hopefully the rot doesn't go beyond the sheeting.
The good news is that in a few weeks we should have a useable deck. One that our kids can actually go out on. One that has stairs from the yard so we can use our kitchen doors to go outside! One that will, hopefully, be so spectacular I'll forget all about missed opportunities to remodel bathrooms.