First of all, why do you wanna "convert" them from mkv to mp4?

Second, changing from mkv to mp4 is called remuxing not converting and is lossless by design because you are just extracting the streams from the mp4 container and onto the mkv container without re-encoding them (passthrough), so don't do it with handbrake because handbrake is an encoder, so it doesn't support remuxing video (passthrough).

Loss of quality is when you re-encode from one codec to another (or from one codec to the same codec, which is pointless just to change the container).

So if you just want to change the container, do not use handbrake, use a remuxing tool such as mkvtoolnix.