[KevinH]

Those are not links. Those are "data-" extra custom attributes being applied to a div tag. These are meant to be read only by an underlying javascript or in css. These are not pure urls either as they are not properly url encoded (using a name full of spaces is generally not a good idea across multiple readers). Sigil will not auto update any of these custom attributes when you use Sigil to rename a file as they are just a set of custom data being passed to something else (in this case a javascript) and there is no way for Sigil to know what those custom attribute values represent.

A div can not actually directly html link out according to the spec. Instead to create an html link you must use a anchor ("a") tag with href or an object tag, or iframe or ....
Are you actually trying to create an html link?

Have you linked the javascript properly inside the head tag?

As for your second issue, not that I know of. But as filenames are not seen by e-reader users, why not just rename the mp3 and vtt files to some generic name in each book.
Or use a batch script to build the epub on the fly from the command line with any info you want. Or instead pass manifest ids and then your javascript could just parse the opf to get the current filenames with those manifest ids.