Rob:
DT is designed to be able to import and recognize text content in a wide spectrum of file types, as well as a number of image and multimedia file types.
You can access a complete list of the supported file types from the DT Help menu: choose DEVONthink Help, which will open the Help file. Then click on the item named "Supported file formats." You will see a large list of supported files, for which DT has been designed and tested. New file types are frequently added with updates of DT, and the list of supported file types will continue to grow.
What happens if you try to import a file type that’s not on the supported list? Sometimes, nothing. DT will refuse to import the file.
But files that are really packages are a special case. CP NoteBook notebook files, NoteTaker notebook files, Create documents and KeyNote presentations are package files. Packages are really folders that contain other folders and files – and that’s the way DT treats them. The result of importing a package file into DT may be unpredictable, and trying to export the import out of DT to recreate the original package probably won’t work (although I haven’t played with this). DT didn’t "damage" your notebook file; it simply read it the way the operating system told it to do, but the result wasn’t an operating CP notebook.
I’ve got both CP NoteBook and AquaMinds NoteTaker, and I’ve got a lot of notebooks generated under these applications. I don’t try to store them as notebooks in DT – they stay in the Finder. (Another neat thing about NoteTaker is that I can do a contextual menu search on a term or phrase while I’m in DT, and open the related NoteTaker notebook(s) – and vice versa, of course.)
If I want to import part or all of a notebook’s contents into DT, the easiest and most reliable method is to print a page or a notebook as a PDF file, and Index import that file into DT. Actually, I do most of my notebook work with NoteTaker, because it lays out PDF files better than does NoteBook. In reality, I’ve taken to doing most of my writing in DT and use NoteTaker as one of my vehicles to layout and "publish" final output in PDF or HTML.
One more note: Although DT can in large measure serve as a Finder replacement for document storage, I choose not to physically import my important PDF, Word and image files into DEVONthink. Those files remain intact on my drive – I simply import their text content into DT. However, I do store all of my HTML, RTF, RTFD and text files inside the DT database. DT permits the user a wide range of choices.