Perhaps the Windows error is correct in that you did indeed remove the unit before an update got completely written to flash memory. (always use the Hardware Device icon or Home's Device Disconnect icon).
In any event, while it may be a false positive. you could allow it to so do.
But, another way, from a command prompt is to run chkdsk X: /f where X: represents the drive represented by TomTom.
Also, Windows gets confused with files with the extension of .chk and thinks they are Windows' file recovery fragments. But, tomtom's app is linux based and, as such, files with this extension mean quite something else entirely.
In fact, if you delete them, your app will not run.