What do you mean by "now"?
IIRC we never cared about CRLF or LF for this script and nobody ever reported such problems. That doesn't mean there isn't a bug there but I personally consider it unlikely to be related to the line endings. I personally tested self-deletion of the script quite a lot and usually it works.

Probably the left geany_run_script_XXXXXX.bat scripts are caused by something else.

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