How to Recover Lost Emails on iPad After Changing Password

From what I read, you actually are almost there. It looks like your problem may be how the folders are done (as in, locally or on the server).

As you said in your answer, you copy the emails to local folders, so therefore they would never be on your phone. And with iCloud's limited rules (in the cloud), as you note, you cant really make a sound or do much with them either.

As long as your Mac is always running (to run the rules), you really would only need to update your local mail rules to put the emails in the servers folders. This way if you are at your computer, you would hear the audio cues, as well as have the mail filtered. If you step away, as long as your Mac could still process the mail, it will copy the emails to the correct server folders, and be available.

On your Mac now, you should see two inboxes, iCloud and 'On My Mac'. Make sure folders exist under the iCloud account for where these messages should go. Then update your rules to point to the iCloud account folders, versus those on your mac.

The only thing you may see from this is some messages will be in your inbox for a very short period of time (before your Mac runs its rules), versus iClouds server side rules that process mail before its delivered.

Sure, You could use the iPhone Configuration Utility or Apple Configurator to create a profile for the server settings.

Once you've gotten a signed profile document (it can be self signed if you haven't set up trusted SSL certs, etc…) you can email it or post it to dropbox or otherwise put it on a web server for each device to retrieve.

The users would tap the file to download it and then tap to accept the payload. You could leave the account blank so each user would just have to enter an account/password and the profile would have the details on the mail server and settings to be installed.

Start with the deployment page at Apple and scroll down to the Configure section to read more on MDM and Configurator.

http://www.apple.com/iphone/business/it-center/deployment.html

Reading into your settings, you might also consider using directory services or a single sign on solution to pull a person't correct email account from a central directory, but that might cost more than a one time, touch all 50 devices exercise. In the end, you might pay for automation software since it allows better reporting and flexibility as changes like these tend to come more and more often in most businesses.