I think a script that converts mkv to mp4 should not delete original files. User can do that by himself if he decides that the he is glad with the converted result and doesn't require original files, what if the result turns out to be corrupted somewhere in the converting process. Then all my data is lost! Furthermore, for some like me, I like to keep all sources just in case.

That being said, I do see this feature being useful for some people, so I think the best choice would be to introduce a prompt asking user if he wants his original files to be deleted and the default choice should be "No".

You can't just delete user's files without asking him.

When I run (the latest ver. ffmpeg as of this post) the following:

_ffmpeg -i /INPUTFILE.mkv -codec copy OUTPUTFILE.mp4_

The subtitle stream is not copied over.

INPUTFILE.mkv details:

Input #0, matroska,webm, from 'INPUTFILE.mkv':
Metadata:
creation_time : 2022-06-19T09:43:26.000000Z
encoder : libebml v1.4.2 + libmatroska v1.6.4
TITLE : Encoded By: mkvAnime
Website : Google Search - mkvAnime.com
Duration: 02:21:53.31, start: 0.000000, bitrate: 4073 kb/s
Stream #0:0: Video: h264 (High), yuv420p(tv, bt709, progressive), 1920x804 [SAR 1:1 DAR 160:67], 24 fps, 24 tbr, 1k tbn (default) (forced)
Metadata:
title : mkvAnime
BPS : 3432045
DURATION : 02:21:53.167000000
NUMBER_OF_FRAMES: 204316
NUMBER_OF_BYTES : 3652196555
_STATISTICS_WRITING_APP: mkvmerge v62.0.0 ('Apollo') 64-bit
_STATISTICS_WRITING_DATE_UTC: 2022-06-19 09:43:26
_STATISTICS_TAGS: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
Stream #0:1(hin): Audio: ac3, 48000 Hz, 5.1(side), fltp, 640 kb/s (default) (forced)
Metadata:
title : mkvAnime
BPS : 640000
DURATION : 02:21:53.312000000
NUMBER_OF_FRAMES: 266041
NUMBER_OF_BYTES : 681064960
_STATISTICS_WRITING_APP: mkvmerge v62.0.0 ('Apollo') 64-bit
_STATISTICS_WRITING_DATE_UTC: 2022-06-19 09:43:26
_STATISTICS_TAGS: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTES
Stream #0:2(eng): Subtitle: subrip (default) (forced)
Metadata:
title : mkvAnime
BPS : 56
DURATION : 02:11:49.833000000
NUMBER_OF_FRAMES: 1950
NUMBER_OF_BYTES : 55494
_STATISTICS_WRITING_APP: mkvmerge v62.0.0 ('Apollo') 64-bit
_STATISTICS_WRITING_DATE_UTC: 2022-06-19 09:43:26
_STATISTICS_TAGS: BPS DURATION NUMBER_OF_FRAMES NUMBER_OF_BYTE

OUTPUTFILE.mp4 details:

ffprobe -i OUTPUTFILE.mp4
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from OUTPUTFILE.mp4':
Metadata:
major_brand : isom
minor_version : 512
compatible_brands: isomdby1iso2avc1mp41
title : Encoded By: mkvAnime
encoder : Lavf59.27.100
Duration: 02:21:53.31, start: 0.000000, bitrate: 4079 kb/s
Stream #0:00x1: Video: h264 (High) (avc1 / 0x31637661), yuv420p(tv, bt709, progressive), 1920x804 [SAR 1:1 DAR 160:67], 3432 kb/s, 24 fps, 24 tbr, 16k tbn (default) (forced)
Metadata:
handler_name : VideoHandler
vendor_id : [0][0][0][0]
Stream #0:10x2: Audio: ac3 (ac-3 / 0x332D6361), 48000 Hz, 5.1(side), fltp, 640 kb/s (default) (forced)
Metadata:
handler_name : SoundHandler
vendor_id : [0][0][0][0]
Side data:
audio service type: main