With newer data loggers, such as the CR1000, the default output file format is TOA5. This format requires that a header be present that accurately describes the data that will follow. LoggerNet cannot append to this file format without first checking the header of the existing file. If that header disagrees with what LoggerNet knows about the table, it will back up the existing file and start a new one with the proper header.
If it is not desired to have this checking take place, the format of the file can be modified in LoggerNet by specifying the Output Format field for the table as ASCII Table Data, No Header or Array Compatible CSV.