Well try to reset xform 1 object, see if it works. Then, http://www.paulneale.com/scripts/resetXform/PEN_resetXform.htm might be useful, it preserves the pivot. Some exporters are very picky with xform.
Noors, I owe you a pint :D You have made my weekend! I've not tried it beyond a few objects yet but it seems to be doing exactly what I need. A clever little script. And it makes you wonder why over the years reset x-form hasn't been improved to function like this to begin with. Reset x-form always feels so destructive…