Last_run_metadata_path file is not updating but sql_last_value is changing in every scheduled time

I have my logstash setup on linux server. I have made two config files,
One file is for pulling the entire records from sql server table and other file just update the the new changes.
When I run the first file manually by direct command my last_run_metadata_path file gets updated with the timestamp.
But when I run the second file by linux service it takes the value from the last_run_metadata_path file and even sql_last_value keeps changing in every scheduled time but that values does not update in last_run_metadata_path.
Any help would be appreciated. Thank you!

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