Using VLC to convert a 10 minute 25fps h.264/AAC mov file to m4v, keeping original video and audio (no subtitles), I notice that the last 2 frames are missing (file is 2 frames shorter on end), compared to using MPEG Streamclip which converts the entire file (save as mp4) exactly the same length as the original. This makes it unreliable to use for this purpose and would seem to be a bug.
MacOS Mojave 10.14.6. VLC version 3.0.11.