Perhaps in the "non-Tk script" you can include an END{} block - something like:

END{$obj->Kill($exitcode) if $obj->GetExitCode() == STILL_ACTIVE};
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For that to work you'll need to be using version 0.10 of Win32::Process and you'll need to load the module as:

use Win32::Process (STILL_ACTIVE);
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Even with earlier versions of Win32::Process there's probably a way of doing it - assuming that the END{} block is the way to go - which I've not properly tested. In fact you might even find it sufficient to simply:

END{$obj->Kill($exitcode)};
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which would work for earlier versions of Win32::Process, too.

Also check the syntax of the GetExitCode() call (if you find you need to use it). The docs have it written as

$ProcessObj->GetExitCode($exitcode);
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but supplying an argument doesn't smell right to me.

Cheers,
Rob