I'm working on a large iBooks Author file. About 100 pages in, when I went to save it, it said Document Could Not Be Saved. I don't know if it is because of the size of the document, the shape that I added to create a mask over text, or the odd paragraph styled that I redefined.
There isn't a Save As feature and you can't export to an .iba file.
It turns out that File > Duplicate is the same as Save As, but that isn't straight forward. I was able to Undo for several steps and then save it.