Youtube supports several basic forms of subtitling for videos, but the most advanced form comes from their YTT / SRV3 file format.

This format supported options not available in any other subtitle format. This includes bold/italic/underline, custom colours and transparency for both the text and the background box, outlines and drop shadows, alternative fonts and font sizes, precise positioning anywhere on the video, vertical text and ruby text for Asian languages. (List taken from this helpful user report post: https://www.reddit.com/r/youtube/comments/1qdvgmc/uploading_srv3_subtitles_got_brokendisabled/ )

The use of this format was necessary to generate subtitling that matched actual text on screen and natively replaced it, generate subtitles that were coloured to match multiple different speakers so they were easily identifiable, and more.

Some examples of use include (horror movie content warning for these vids):

https://www.youtube.com/watch?v=eHcHjcV8SNY - "Unconscious Requiem" in which the subtitles flicker and change colour to match the flickering and unfolding text on screen

https://www.youtube.com/watch?v=3iUgKH8c7p4 - "Retry Now" in which the subtitles are styled to match the dialogue as it appears in the visual novel text boxes on screen

Users are now report submitting their videos with advanced subtitles does not work.

This doesn't just disable it for new videos - some users are now reporting that old videos are having their custom subtitles removed, including ones with 10M+ views.

Hopefully this change gets reverted, but you should download subtitles off any video you wish to keep.