Rewrap MKV to Mp4 Losing subtitles

I've been rewrapping all of my MKV files to mp4 so that they're supported by a VR headset app. Only downside I've discovered after doing a ton of these, is that the subtitles that were in the MKV files don't come across over the mp4 files. Is there any setting or other method I could do to keep the subtitles but yet not have to completely re-encode the video? Thanks!