Initial findings for Prepar3D v3.1:
 

First update since the last major delivery in November 2015, this major version is already available on the Lockheed Martin site (http://www.prepar3d.com/purchased_downloads) in two forms:

•     that of a full version (recommended by LM) or
•     Individual Components download

Take all of the version in case (as a single zip or more packages separately) but I confirmed that it was entirely possible to upgrade a v3.0 and without significant problems: the experiment was done on my own machine.

How to do ?

• Connect with your credentials on the link given above, 
• In the "Downloads" you will find three sections  

1. for the full version in a single zip (Full Download)
2. one of eleven separate packages (Individual Component Downloads)
3. and the SDK (Software Development Kit (SDK)).

• Personally I prefer to take the version in separate packets, easier to download because if there is a PB on one dowload it's more easy to resume. 
• If you opt for the full version, it will unzip it into a separate folder to dispose of eleven components. 
• For the update of version 3.0, the file we are interested in is Install_client.msi (123 MB).
• Remember to save your file settings of the earlier version:

1. C:>Users>"user">AppData>Roaming>Lockheed Martin>Prepar3D v3
2. C:>Users >"user">AppData>Local>Lockheed Martin>Prepar3D v3
3. C:>ProgramData>Lockheed Martin>Prepar3D v3

• Via the Windows Control Panel, in the section Programs and Features select from the list Prepar3D Academic client (or equivalent) 
• Uninstall the client takes only a few seconds ....
• Then run the previously downloaded file Install_client.msi and wait a few seconds / minutes
• WARNING that you select the directory where you installed the v3.0 ... because by default, the program offers a directory C: and my P3Dv3 is on S: so be careful!
• Once the installation is complete, remember to "clean your shaders" and then you can restart P3Dv3.1.

PS: Shaders are located at C:>Users>"user">AppData>Local>Lockheed Martin>Prepar3D v3>Shaders"

• A window will appear asking you to activate the product, select "Activate Online" and enter your password (those used to log in LM)
• And here it is finished.

IMPORTANT: At launch, if you have Orbx scenes P3Dv3.1 will ask you if you want to run the libraries (DLL) ObjectFlow. To the extent that they have been updated at the time of this writing, you can accept.

Updates Install_Content.msi and Install_Scenery.msi and are not necessary in the first place. These updates relating to:

         A positioning of the lights changed to fixed virtual cockpit on the Beech Baron
         Additional updates to the India Fox Echo F-35A
         A change in the behavior of ships compared to the waves

         Minor changes in five airports in the southeastern US
         Update coasts, lakes, rivers and elevations in Singapore

These additional content correct a few specific points on the ship wakes and behavior.

If you want to add this ships's behavior and you have not installed the Content.msi but only the Client, you'll need to adjust the * .fx for all vessels used by P3D or wait until the various developers adjust their files and publish them.

For each file in ...>Effects>fx_wake*.fx and for each item [Particle.x] you must add the variable Ground Decal=1

[Particle.0]

May have to be adapted effects on some boats.