Thank you all for the suggestions.

@Michael : indeed that works great - with UseSimpleEntities=n, all the problematic elements that the cutter software wasn't seeing are now properly imported. Perfect :)
Is there any way to have this is part of the export settings, so as to not have to tweak the ini each time ?

Also, is there any way to perform this kind of conversion without having to even export/reimport at all (that is to say, getting to the result from within the work scene) ?

@Blowlamp : well this approach works to an extent, and I have been doing exactly that when needed ... but is not sustainable when having to redraw all the through holes of a design :) And moreover, one could end up missing some important parts.

@Bemfarmer : I'll definitely have to try this idea too, thanks !