This comes too late to help the original poster, but perhaps it will help someone else.
This bug occurs not only with NSCollectionView. It occurs whenever one of the subviews of a split view itself has a subview. It is easy enough to reproduce, and there is no way to fix this within Interface Builder. This is an old bug, which I encountered years ago, but at that time was not able to solve.
Make a copy of the xib file before unembedding the split view. Do the unembed and save the file, which is now totally corrupted. Next, open the copy and the corrupt version in a text editor, so that you can look at the XML. The corrupt file will have view frames that are very strange, with heights and widths that are zero, or y coordinates that are large negative numbers. Many views will have no frame property at all, which is probably why the frames cannot be fixed in Interface Builder. Luckily, all the missing and corrupted frame rects have valid properties in the original file, the copy you made before the unembed. Simply copy these frame rects from the original file to the corrupt file and save. Voilà. The previously corrupt file now opens correctly. You may have to move things around, or reapply constraints to get things back to where they should be. But this fix enables you to edit the layout normally again.