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The way the PDE/p2 branding works, the client provides a .ico file, and we replace any image in the .exe that has an exact matching size in the ico file. If the client does not specify a particular size, they get the "default" launcher icon. This means that a product using this branding against an eclipse.exe with the new 256x256 icon will end up with the default eclipse icon in most cases (Windows 7 will select the 256x256 icon in many cases). We should have a porting guide entry for 4.2, stating that clients should add a 256x256 icon to their .ico file for their branded application.
This was already released two weeks ago: http://git.eclipse.org/c/platform/eclipse.platform.common.git/commit/?h=R4_HEAD&id=d97c545cfd6130477aa4222ad97488668ff93efc