Depends on Bitrate, what has on the MKV - what is on the new file (for video)
what audio tracks did you include, the same as the MKV or just one etc...
ive been searching and experimenting but can't find a solution. what is the best format and best way to convert mkv files to work with iTunes while preserving the best video quality?
Load in the MKV file in to Handbrake, use the Appletv preset, put what ever bitrate you want for the video, set the audio to one or 2 tracks, most people have track 1 AAC and track 2 AC3 pass thru.
Go Go Go, sit back and wait. Play file, enjoy. . .