The -p command line option should take a list of property files to be applied in order. This would allow the default JMeter property file to be left alone and custom properties to be read from a subsequent file.
New option -q (--addprop) added. Multiple additional files can be supplied if required. Code change added to 2.0 branch
This issue has been migrated to GitHub: https://github.com/apache/jmeter/issues/1514