Why is there discrepancy a Scan Size?

Application ear file which you uploaded is like raw file and may contain xml files , pdfs , gif (images) etc which are not scanned by the veracode scan engine. After prescan, scan engine removes these and determines the exact scannable code which might be less than the actual uploaded file. 
Also if there are javascript files within EAR , those will not be extracted , so it is important to upload javascript files separately. 

Please note after the scan , PDF report will have Scope of Static Analysis which shows modules included in the application scan. 
 

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