Some time ago I upgraded from Magento 1.4 to 1.9... a good part of the upgrade being done manually due to the huge gap covered and an extension that updated the core. It took some time, but the instance is solid and working well... with one exception: some option groups from Configuration have been eliminated without trace. See a couple of examples below:
... but there are more in different areas. The thing is that their corresponding configurations work ok, just the possibility to manage it is gone: for example, the free shipping settings work ok in the website, but I have no longer the item available.