When you call your second command, it's not done in the environment you modified in the first command. In fact, there is no environment remaining from the first command, because the shell used to invoke "environment_defaults.sh" has already exited.
To keep the context of the first command in the second, invoke them in the same shell:
system("source environment_defaults.sh && obe");
Note that you need to invoke the shell script with source
in order to perform its actions in the current shell, rather than invoking a new shell to execute them.
Alternatively, modify your environment at the beginning of every shell (e.g. with .bash_profile, if using bash), or make your environment variable changes in perl itself:
$ENV{FOO} = "hello";
system('echo $FOO');