The help says:

"Pause after downloading..

This option lets the engine do a pause every time it has retrieved a specific
amount of bytes
Useful if you are mirroring a site bigger than the available space: you can
then backup and erase the downloaded files during the pause"

But doesn't say which files can be moved. 
I am doing a download of a site and at present there are 40,000 html files in
one folder. If, while paused, I move some of the html files to a different
folder, is that OK or they be redownloaded as missing?