Since Calibre will automatically strip out the hyphens given any Edit Metadata chance to do so, you could temporarily add the hyphens, then immediately copy part of the ISBN into a custom column using Bulk Metadata Edit Search & Replace.
This SQL will work in any SQLite tool, such as 'SQLite Expert-Personal' (which is free) to add the hyphens before you use BME S&R.
Code:
UPDATE identifiers SET val = (SUBSTR(val,1,3)||'-'||SUBSTR(val,4,1)||'-'||SUBSTR(val,5,3)||'-'||SUBSTR(val,8,5)||'-'||SUBSTR(val,13,1) )
WHERE type = 'isbn' AND val NOT LIKE '%-%' /* AND book = 25376 */ /* example output: 978-0-684-84328-5 */ /* These are comments /*
You can remove the comments around the 'AND book=nnnnn' while you test if you wish to impact only a particular book.
DaltonST