I think I get the general picture - though I'd have to see the kit in person to understand all the details. It sounds like you're the victim of a typical Hellerism. As I've said several times before in this forum, the people who designed those kits seem to have been superb artisans whose understanding of real ships was, to put it as gently as possible, defective.
To do a really thorough, accurate job of rigging a model like this really requires a good set of plans. I think I recall that Jean Boudriot published a volume on La Belle Poule, and there's a package of plans for her in the Musee de la Marine series, which is available in the U.S. through Taubman's Plan Service. Unfortunately both of those sources are pretty expensive; I can't blame anybody who balks at the prospect of paying something in the neighborhood of a hundred dollars on a modeling project of that nature.
I think I have seen a few cases (not many) of chainplates effectively crossing each other between the channel and the hull. It can happen when the aftermost shroud deadeye is close to the first topmast backstay deadeye. The shroud is on a steep angle and the backstay is almost vertical, so the chainplates cross. (The backstay deadeye is probably a little inboard of the shroud deadeye, so the chainplates are clear of each other.) Maybe that's what's going on here. But it's just as likely that Heller simply made a mistake, through lack of understanding. The idea of two chainplates being held to the hull by one bolt (i.e., coming out through the same hole) seems highly unlikely, but I don't suppose it's impossible. It's a pretty safe bet that the shrouds and backstays aren't supposed to run in front of the gunports. The standard approach was to space the deadeyes in the channels so that wouldn't happen. That's why the spacing between the deadeyes of warships is frequently inconsistent.
If I were doing it I think my inclination would be to fill all the questionable holes and drill new ones in locations that make sense.
One approach to the deadeye problem that you might consider is the old-fashioned "combo unit." "Deadeye combos" used to be standard fare among wood ship model manufacturers; I'm pretty sure Bluejacket ( www.bluejacktinc.com ) still makes them, and Model Expo ( www.modelexpoonline.com ) may sell them as well. A deadeye combo is a pair of deadeyes cast in metal, complete with cast metal "lanyards." The idea has its limitations - mainly the fact that the linear spacing between pairs of deadeyes in a gang of shrouds varies quite a bit. But it might be worth looking into. You also might consider the old "blob-of-glue" trick. On such a tiny scale a drop of Elmer's glue, with some black acrylic hobby paint mixed in to stiffen it, can make a fairly convincing deadeye if it's applied carefully. Another, slightly more difficult approach is to slice off thin slivers of plastic rod and glue them to the shrouds. On 1/200 scale the key to success is to give the viewer the impression that the deadeyes are there.
I'm afraid this hasn't helped much. But good luck.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.