kill -SIGCONT $program
If you program is daemon, this work. But, if is not daemon - use:
jobs and bg - if you need backgroung prog running, or fg - if need foreground running. How?
cynic@ubuntu:~# jobs
[1]+  Stopped                 vim /etc/lighttpd/vhost.conf
cynic@ubuntu:~# fg %1
vim /etc/lighttpd/vhost.conf
I think - you can put a flag in the first script, for example, AUTO = 0. If you send sigstop from a script - AUTO = 1, and then you can start from this option - check - whether manually shut down the program or script.