lets the module has some bundled libraries. On Make performing these jars are written to 'bundles' folder and get manifest updated.
Don't clear the output directory; make some changes to the LibraryBundling settings (change some manifest entries)
Now run make: you get errors like following one:

There was a problem when trying to bundlify file://C:/VelocityTools/velocity-tools-1.4-src/lib/velocity-1.5.jar: java.io.IOException: Failed to create child file at C:\Documents and Settings\Irina.Petrovskaya\IdeaProjects\osgi\libs_bundling_test\out\production\bundles\velocity-1.5.jar\tmpbnd179116589103537220.jar

the jar manifest is not changed.
You should clear the directory to make changes possible.