A way to preserve softsubs and multi audio formats in MKV video format

[bungadrum]

I tried converting a MKV video to a MP4 and MKV lower quality to save some disk space everything worked fine, but the video had softsubs built in and when you convert the format the softsubs are gone. Is there a way to add a option for softsubs and multi audio files in mkv videos to stay preserved when you convert them to a lower quality? For hard subs everything works fine, but soft subs are a hassle when you want to downgrade to a lower quality.