When running an upgrade from SmartConnect 9 or 10 to SmartConnect 2010 a separate upgrade process must be run to update the maps. In certain instances, the upgrade window can be blank, or have large red Xs on the window as appears here:

The resolution is to go into your Great Plains Dynamics directory and copy 2 dll files from there to the SmartConnect directory.
1. Using Windows Explorer, browse to C:\Program Files\Microsoft Dynamics\GP2010 directory
2. Copy the following 2 files:
Microsoft.Dexterity.Bridge.dll
Microsoft.Dexterity.Shell.dll
3. Paste them into your SmartConnect folder where the eOne.SmartConnect.Upgrade.exe file is located. This is normally in the C:\Program Files\eOne Solutions\SmartConnect directory.
4. Relaunch the eOne.SmartConnect.Upgrade.exe file and it will function correctly now.