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Once FreeRIP is in Converter mode you can use File->Add files to convert... menu option to build the list of WAV (or other audio format) files to convert. Alternatively you can use Windows drag&drop: drag audio files from a folder and drop them onto FreeRIP window.
Once the source file list is complete, use Rip menu to convert them in the chosen output format. E.g. select Rip->Convert selected tracks to FLAC to convert selected tracks to FLAC.
For more details about FreeRIP Converter options, look here in FreeRIP user manual.
Related resources: Download FreeRIP MP3