Why does Weatherlink cannibalize it's files?
Weatherlink almost never does that. The usual cause is file corruption (bad disk drive sectors, killing software improperly, etc.).
How do you shut down your computer? (Or are there frequent power failures, etc.?)
Is there any way to recover the data?
Depending on your type of logger, archive interval, etc. - for
recent month or two, shutting down Weatherlink, deleting the corrupted .wlk file, and restarting WeatherLink may recover the data (from storage in the logger).