When you install the Maya FBX Plug-in, it installs two instances of the plug-in: the actual FBX plug-in that is copied to the source directory (C:\Program Files\Autodesk\Maya2011\bin\plug-ins) and a copy that is stored in the FBX folder that you specified during the installation.
The installation screen that specifies a destination folder
When you uninstall the Maya FBX Plug-in, the uninstall process only removes the plug-in copy from the from the destination folder you specified during the installation. To remove the FBX plug-in completely, you must delete it manually. The reason you must perform a manual deletion is because the FBX plug-in is a part of the default Maya installation.
Essentially, when you uninstall, you remove the contents of the FBX backup folder, for example, C:\Program Files\Autodesk\FBX\FBXPlugins\2011.2\Maya 2011 64-bit, as well as any related entries in the Start menu.
It is good practice to keep the previous version of the plug-in, especially if you are working on a project where the workflow is heavily dependent upon the plug-in. If the newer version of the plug-in disrupts your process in some way, you can revert to the previous version. If you do not want to lose access to the FBX plug-in that ships with the Maya software, select Yes when asked if you want to accept saving copies of the old plug-in. This option occurs whenever you install newer versions of the FBX plug-ins.