Note: As of version 0.94, Pakrat can automatically update embedded .nav files in a BSP. So if you use Pakrat to embed your custom files, you don't need Navfixer.
Navfixer is a simple little program that fixes the annoying "Navigation Mesh was built using a different version of this map" message that appears if you try to embed a navigation (*.nav) file into a HL2/CS:S BSP mapfile using BSPZIP.
Navfixer is a stand-alone windows console program. You do not need Java to run it. Download it here and unzip it into any convenient folder.
To use the program, build the map as normal, generate the nav file, and embed it in the bsp using bspzip (or an alternative program such as Pakrat).
Now, drag-and-drop your .bsp file onto navfixer.exe. If navfixer finds the embedded .nav file, press "Y" (yes) to update the file. The corrected file will be loaded without the "navigation mesh" message.