For groups, to flatten the transform, ungroup the moved group, and regroup it (keep the same selection) - it's done rather quickly with keyboard shortcuts Ctrl+U, Ctrl+G. Watch out for transforms of parent groups (if nested), though and transforms on parent layers (after resizing the page or changing its orientation).

This works. I already had transforms set to 'optimize' in preferences.

Of course I have 60+ groups on an average map so I'll look to scripting this as an extension but you've pointed me in the right direction.

Thanks.