I'm getting the hang of this and have drawn up some cave. It went OK until I got to a complicated section, with an underlying streamway adn overlying passages. The streamway needs to be a separate scrap. But I haven't got that far. One bit of wall wasn't shown. By adding a map-fg colour I could see that therion is very confused about what is the inside and what is the outside of the scrap.
Only minor improvements were required -- mostly to correct line types (the hidden wall was actually a border, the inner pillar should have -outline in option...). All my changes are marked red in the enclosed picture. The correct line types make correct scrap joins possible. Simple join s1 s2 worked fine with one exception, where the scrap ends are too far. There is perhaps a blunder in your data. Martin