What is your script doing? Some realtime background processing?

I'm not familiar with 2.49 API, and I'm not sure if this helps your
case, but here's my suggestion:
perhaps you can pass all the relevant data to the new instance of the
script (which would continue the job), and the old one would shut down
itself? I used a similar approach during the development of one of my
scripts, though it was 2.5+ API.

For what reasons are you still using 2.49, by the way?
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