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Use daemon mode, delegate each Django instance to a separate set of processes, and set python-path against each daemon process group as required for each. See:
- http://blog.dscpl.com.au/2012/10/why-are-you-using-embedded-mode-of.html
- http://blog.dscpl.com.au/2012/10/requests-running-in-wrong-django.html
Otherwise set the sys.path in the WSGI script file and not in the Apache configuration.
Source:stackexchange.com