OS X Lion Server app reinstallation on 2011 Mac Mini Server I have had purchased for me by my employer a new Mac Mini Server. It came pre-installed with Lion Server (the Server app from the App Store that costs $49.99).

Upon opening the App Store, other preinstalled software (iPhoto, iMovie, Garage Band) was instantly added to my Purchased tab, giving me the licenses to these applications on my Apple ID. However the Server app still shows up as a $49.99 purchase rather than saying "Installed" and is it not listed under my Purchased tab.

If I were to reinstall the operating system, how will I install the Server app without paying the $50 to get it from the App Store again?
When you boot into the recovery partition or use internet recovery - Lion will be granted as a download according to the serial number of the mac. My suspicion is server will be handled in the same manner as the OS, not as he iLife apps are granted to an Apple ID.

You will have to pay for Lion Server if you want it associated with a specific Apple ID (just like Lion) - but shouldn't have an issue when downloading to that mac.

You can test this by booting to recovery (in any of the manners) and re-installing Lion and Server to a new USB external drive.