The first thing I do when dealing with metadata is remove the ISBNs. They never correspond to the physical book I have (I buy physical books all over the world). They just get in the way.
I have considered building a tweak that would prevent the box from ever being filled in, and/or adding a 'clear ISBN' check box to bulk metadata edit. Haven't done either because Kovid has said he will eventually build a general solution to the download metadata choice problem.
I suppose I am voting that you leave it like it is: not merge ISBNs. If you feel you need to change it, make the behavior tweakable.