I've built literally dozens of Enterprise systems for sharing and/or web serving. Panorama Enterprise programming is what I do for a living. Along the way I've certainly encountered the issues you're describing but they're often avoidable. There are some routines that can minimize the likelihood or the degree of trouble if there is an issue.
Before updating, make a backup of the Public Databases and a set of the client files. That makes recovery very quick.
Since you have a seemingly high chance of issues, when replacing a shared file, use the Sharing Wizards to take it offline and then to remove it from the server. If you can reboot Enterprise, that's good too. The result is that you're uploading a new shared file versus replacing one. That definitely reduces the rate of incomplete uploads.
That said, one of my clients has some huge shared databases that we reliably update over the internet with only rare issues. (The backups are useful for the times something goes wrong) I use New Generation in the Database Sharing Options to load new versions of the databases and it works very reliably.
Early on we had problems like you're describing but found two causes. The biggest issue was the RAM on the server. It may have just been cheap RAM, or it may have been damaged by heat or power surges; who knows? Replacing it caused the rate of corrupted files to plummet. Later, a better router was installed so that the transfer rate was increased as well as the "cleanliness" of the signal. The result is that corruption issues are now rare with this set of databases.
Regarding your other post on corruption, Force Quitting on a shared system should be discouraged. Too often impatient users resort to it and it does seem to be a common denominator when files corrupt. RAM on client computers should also be evaluated. Look at the logs and see if a particular user shows up when there are issues or the logs show a recovery process was run.
Beware electro-magnetic fields such as a refrigerator, air conditioner or a machine shop in the vicintiy of server, router of client computers. Older ones especially can contaminate the quality of a wireless signal, or of a wired network if the cables run near the motors.