Apparently Public Health England were using the xls file format to upload Track and Trace data into Excel templates. The issue is that this file format can only handle 256 columns and 65,536 rows.  Apparently each test result generates several rows of data (why?) and thus the templates could only handle about 1,400 cases. Anymore than this and the data was just truncated.

The latest version of the Excel file format (xlsx) can handle 1,048,576 rows and 16,384 columns. 

Were PHE using a massively outdated version of Excel? Or were they just incompetent?

In any event datasets such is thus should be handled by a database (e.g. Access or Oracle) rather than a spreadsheet program.