The 5.6 upgrade will evaluate your free disk space, and won't allow the system to proceed with the upgrade if there isn't enough disk space. It also prompt multiple times if you're sure you want to continue, so you could launch the upgrade to see if it has any issues with the pre-upgrade checks, and then quit out of it until you're ready.
Where are the 40GBs? Which partition?
The 5.6 upgrade was successful. The database migration took just under 4 days to complete. The 40GB free space was all on the same disk but i don't know which partition.