I just tried downloading a bunch of my own data files in Excel format (*.xlsx) and they worked fine (i.e., the files were not empty). Thus, I'm not sure whether the problem you are experiencing is due to:
- Something special about your data files, or
- Numbers acting strangely.
Several things you can do immediately to test:
- Try opening the *.xlsx in a different spreadsheet application, such as Microsoft Excel, LibreOffice or OpenOffice. The latter two are open source and available freely. Do any of those also display the files as empty?
- Numbers should be able to read / import the original *.iqdat files as well. Those are simple, tab-delimited text files, and any spreadsheet or statistical analysis application would generally be able to import such files. The only thing you may have to do for Numbers to accept the file(s) is to change the file extension from *.iqdat to *.txt or *.dat.
See e.g.
https://support.apple.com/en-us/HT205391 - The same is true for the 3rd format option, i.e. you can also try downloading your files in CSV (comma-separated values) format. Numbers and other spreadsheet applications should be able to handle those without issue.
Hope this helps.