Things to check:

• Software Update (read the description to see if it fixes the issue for your OS X 10.7 server)
• Check if OS X 10.7 Server requires its Time Machine to be formatted using Case-sensitive, Journaled Mac OS X Extended. Anecdotally, I've always formatted my Time Machine backup as Mac OS X (Journaled) and Time Machines works fine.
• Check the Permissions. Check that your OS X 10.7 Server user id has access to the USB partition.

For apps that are not sandboxed

Example:

To regain warnings about permanent version storage for Apple Pages

Quit the app, then a one-line command in Terminal:

defaults write ~/Library/Preferences/com.apple.Pages NSDocumentSuppressTempVersionStoreWarning -int 0

– in the Preferences area that's familiar to users of Snow Leopard and less.

For apps that are sandboxed

The operating system uses a different approach to containment of some preferences:

~/Library/Containers/<bundle_id>/Data/Library/Preferences

Example:

To regain warnings about permanent version storage for Apple Preview

Quit the app, then a one-line command in Terminal:

defaults write ~/Library/Containers/com.apple.Preview/Data/Library/Preferences/com.apple.Preview NSDocumentSuppressTempVersionStoreWarning -int 0

Thoughts

I should have thought first of ~/Library/Containers when, in the question, I observed –

com.apple.Preview.plist is not recently modified

– but I didn't realise what was going on until after I used fseventer to visualise writes for a different user of the OS.

References

App Sandbox Design Guide: Migrating an App to a Sandbox

A visual record of me finding the relevant key in the .plist for Pages

A visual record of me finding the relevant key in the .plist for Preview