kellnerp,
I can't say why ours is set up with a checkin directory that is separate from all of the approval directories. I was not involved in the initial setup, which happenned before I started here. As you say, some of our issues would go away if files didn't move around.
I'd LOVE to get all of our directories under 1000 files, but it's a battle I've already fought and lost. There's at least one directory where I don't think it's possible (local copies - which I don't know how to subdivide). Our checkin directory isn't getting that small either without serious rebuilding of how we've configured DBWorks, which won't be happenning in the near future.
Most of those 38,000 checked-in files were never manufactured and never will be. They're either concepts that went nowhere or imported reference parts. A small handful (probably under 100) are files that somebody is currently working on.
As for the replication validation, we've been in contact with our support rep on multiple occasions, mostly about this. I don't know the details because I'm not usually on those calls, but it has been a recurring problem for us. At one point it was due to using an outdated SQL, but I believe that was updated and I'm not sure what's caused our latest round of problems.
I'm sure most of our problems are could be solved by better setup of the program and better admin training. We lost our DBWorks administrator and IT manager last year, and to my knowledge neither has been replaced yet (five months and counting).