The pre-processing does not overwrites original FITS files from the sequence but creates new FITS files with the pre-processed data. The new file names are the same than the original prefixed with pp_ if you leave the default value in the prefix box. Below is an example of pre-processing using offset and dark files. Make sure that loaded sequence is the sequence of your light frames. Also, note that at the end of the process, the new sequence is automatically loaded.