Yes. Try opening that .aup file in Audacity and select 'Export...' (As WAV) from the File menu. If needed, use iTunes (Import) to convert the .wav file to MP3 or AAC etc.
PS,
.aup (AUdacity Project) files are NOT sound files. Your audio data (with edits) is stored elsewhere, unless you inadvertently deleted it. Once you're done with an Audacity project, export it as a sound file for storage; .aup files are not intended for archival purposes.
