Your first step would be to enable the script logging, so you can confirm the load script is showing the correct number of lines fetched for each source you have etc., as I would expect one of your sources is not loading properly, and it may not be an actual error, or you may have used the system variable that ignores errors etc. You can enable the script log via the Desktop client in the app in question by going to Setting\Document Properties\General tab and click the check box to generate the logfile there, save and then rerun things in Azure with that version of the app and check the script log when it completes to be sure the correct number of lines were fetched from each source. You may need to enable the logging on the app on your internal server and compare the two, just FYI. Hopefully this moves you forward here.
Regards, Brett
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