Has the report output file name convention changed between Jaspersoft 6.2.1, and Jaspersoft 6.4.2?
Yes. When reports are scheduled in Advanced Reporting and are asked to output files in "Excel or XLSX" format, the Jasper server 6.2.1, used to include ".nopag" in the output file name. This however is no longer the convention in Jasper server 6.4.2, where ".nopag" is not used, and the file will just be of the <FileName>.xlsx format.
Here is a screenshot of how the report output is, in Jasper server 6.2.1:
And here is a screenshot from Jasper server 6.4.2: