You can extract the classes.dex from the APK then use baksmali to get the smali folder with the command "baksmali classes.dex -o [outputfoldername]"
Then you can put it back into dex by renaming the original (for backup purposes) and typing the command "smali [outputfoldername] -o classes.dex"
please correct me if im wrong i haven't used baksmali/smali in ages.