1. No. We tend to have to open all the AFCAD type files one by one and check them. A very long process.
2. Never eliminate all the .DAT files. That can destroy some gauges. However, the scenery.dat files are temporary scenery caches. FS9 does an extremely poor job of updating them when scenery is removed. If you delete them it will reindex all your scenery, which can be a good thing to do occasionally.
3. Yes a few times.
The first thing I do is sort all the files in the Addon Scenery folder by Date Modified. Then move all the files updated in the last month to a temporary folder outside FS. Run the FS Nav database updater - see if it works.
I move files out in groups of 25 or so to make trouble shooting easier, but if you have like a thousand files, you could move them in groups of 100.
The key is to put the files into small enough groups so you can identify the group with the problem file. Then you can work on cutting that group into smaller groups.
It greatly speeds the diagnostics process and allows you to zero in on problem files much faster.
@ PawPaw's house - near KADS, Addison, Texas, USA