First off, why don't you develop using plain CGI and once the code is done, move over to FastCGI ? That way you dont need to restart all the time.

That being said:

killall my_program.fcgi
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In the usual setup, Apache spawns and controls the FastCGI instances. If one of them dies, it should automatically start a new one. So if you change your code, you could just kill the FastCGI process (rather than the whole Apache) and things get reloaded.

apachectl graceful
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A graceful restart will not cut off currently connected users (not 100% sure if it restarts the FastCGI servers, though).