To set all project properties back to the default value, you can select Project -> Design Goals & Strategies..., and then select and apply the Balanced/Xilinx Default strategy. However, Project Navigator also resets properties such as Macro Search Path and Verilog Include Directories to their default value (blank).
If a process property with a directory path value is reset by applying the Default strategy, the property value must be re-entered for the path to be used.
If you are setting and changing multiple properties, you might want to create a user-defined default strategy that you can use to reset your project.
This issue is resolved in ISE Design Suite 12.2.