OK. The code currently only looks for references of the form '(John 1:x-y)'

From your original post there are other variants of that along the lines of

(Mark 1:16-20; John 1:35-39) two different references
(John 13:23; John 21:20, 24) three references using different separators ';' and ','.
John 19:26, 27; John 20:2-4. No brackets plus two separators ';' and ','.

There is a least consistency in the use of ';' and ',' in the examples you've provided.

Think of the possible confusion to your users when converting the following

John 21:20, 24

I'm assuming that this is two hyperlinks

John 21:20 and
John 21:24

You could have the two hyperlinks as

John 21:20, 24

Note that the comma isn't blue. I think is confusing for a user as its not clear if the second hyperlink is independent to the first.

Alternatively we can convert

John 21:20, 24

to

John 21:20, John 21:24

during the search, which is a bit more wordy but much clearer.

I'm happy to have a look at upgrading the search function but it would be helpful to know what format you'd prefer the output (and also if there are any further variants in how references are provided)