I believe teh 65,000 row limitation is only a problem for older versions of Excel/Office on 32bit Windows. A workaround may be for you to use Libreoffice, or update to the latest MS Office suite.
I'm actually running Office 2013 64bit, but the limitation still exist in the xls format, not in the newer xlsx format, but I did not think the switch could upload that. The real concern is that I can't download the larger file from the switch.
I came across a fix, in My Preferences I changed the download format to csv and the file is complete.
I'm running into an interesting issue and wondering if there is an easy fix or better way of doing this. We have one vendor that has an extremely detailed US rate deck, 168,000+ rows. When I got ready to import it I went to save it in xls format and got an error in Excel that it exceeded the max number of rows, something like 65,000. So I saved it to CSV and then uploaded it. The upload took, the processing was long but once in the rates match quickly and work. Enter the problem though, when I click download the file is an xls file with only the first 65,000 or so records.
I have a work around in mind, but it got me thinking about how I's setting this up and if there is a better way.