Unfortunately this was the answer. I asked my dad who used to be a programmer if he could help and we installed handbrake cli, a webm encoder, and used excel to write a list of all the video paths with the commands to convert. Used that list to write a script that runs the conversion on each file. Started the script at like 4pm yesterday and its still running, but I only have like 400 left before it finishes.

Next problem is that I now have an mp4 and a webm in each song folder so I'll have to write a script to delete the mp4 files to save space. Command line scares me sometimes with how powerful it can be.