Quite interesting. I almost have the same problem (yes, I know, I DO have a lot of troubles with my weather things): I used to work with WeatherLink but the .WLK archive files contain errors which twist the global results, high/low records, etc. So my question is: how did you download the whole .csv file from wunderground? I have two computers so I will try to figure out how to add these old data to my new ones. If it works, I shall of course describe the comprehensive procedure to you.
By the way, we will never say it enough: do backups!
Thanks,