Xilinx ISE Prevent Trimming For CPU
You can prevent trimming with an option on the Map process properties. In ISE, expand the 'Implement Design' section, and right click 'Map' and select 'Process Properties'
Uncheck the option for 'Trim Unconnected Signals' (-u). Click the help button for more information on all the options displayed here.
From the help:

Trim Unconnected Signals
Specifies whether or not to trim unconnected components and nets from the design before mapping occurs. Leaving this option blank is useful for estimating the logic resources required for a design and for obtaining timing information on partially finished designs. When implementing an unfinished design, set this property to False (checkbox is blank) to map unconnected components and nets.
By default, this property is set to True (checkbox is checked), and unconnected components and nets are trimmed.