Import parser on a Batch File

Hello, I've successfully set up an automatic upload using the Harvest Folder. However, I want to use the Skipline functionality within the file to reduce the import size.

This works perfectly when I manually import the file into the specific Import Step. But when using the automatic upload via the Harvest Folder, the Skipline functionality doesn't seem to be applied.

Does anyone have an idea for a possible workaround?