I think you should be fine. just make sure you keep audio to the rest and you should be fine
The rules require you to have audio for all the run.
It can't be helped if YouTube decides to mute the audio. The only solutions to that are move to a different video sharing platform, have a music mod with non-copyrighted music, or for the mods to have a special circumstance for these songs.
I dont agree with just muting out long parts of the run. I havent seen youtube mute out parts itself and yeah you can use music mods
iirc you can replace songs when it finds copyrighted music and it mutes the audio until you do that so that does exist.
Recently, Twitch has announced that on April 19, they are removing highlights from accounts that have over 100 hours of highlights (until you are below 100 hours). This means that if your Twitch account has over 100 hours of highlights, your runs on speedrun.com are at risk of losing its video foota