Sorry for the late response.
@BMu33
Because I did not do that.
I had to re-download the files because I formatted the drive they were first completed on.
@Guest
what do you have the 'file allocation' set to? Settings-Transfers-Files
Sparse (default)
Windows 7 x86
how are you deleting the files? through tixati or os?
I formatted the drive, the files were lost.
I had "Error on missing downloaded files" disabled but that isn't a factor since I tried with it on and deleted a blank, checking file only for it to start checking again.