Hi Garry!
Thanks for yours fast and detailed answer.
It seems that my research ability needs to improve, since I couldn't find the existing issues about the importing pages in mantis. In your link is allready the bug described. If i find something else during the importing, I will try to reproduce it and add it in the comments of the existing bug issue in Mantis

When you say "the best option to avoid big mistakes is to layout every chapter in a different document", what problems are you trying to avoid?
The normal stuff: if you have a large document it could happen that the program crashes (though it happens rarely) and it wasn't yet saved. Also if you press some keys without willing it or knowing it, you may change the whole document, not finding what happened till it is too late. Those are only some examples. Also Scribus works (of course) much faster using smaller documents.
For the moment I think the best solution for large projects is yours: spliting in documents the project, semi-manual numbering, manual TOC, and merging the pdfs with an external tool. I have not tried it yet, and I only wonder how good are those tools in creating pdf documents for professional printing. Personally I really like Scribus precisely for its power when exporting and its color management. For instance it is the only libre software I know which can export in CMYK and RGB, and even select the desired ICC color profile.
In the future would be nice to have a kind of Master Document, to have all the documents within it, refresh all the data within a button, synchronize master pages and styles, and finally exporting the whole project (
http://forums.scribus.net/index.php/topic,2620.msg12132.html#msg12132)
The project I'm working right now is about 210 pages, and I'm allready merging all the documents in a final document, to export it and send it to the printing house. Scribus works a bit slowlier, but still good enough. If everything goes smoothly, I may add two books really soon to the succes stories! By the way, there are wonderful works done over there with Scribus!