If I shut down my MacBook and don't wait 60 seconds have I stopped it saving to iCloud?
There's no need to wait 60 seconds before using the "Shut Down" feature in the top menu.

When you save documents and close programs, the data is saved to disk. When you use "Shut Down" the system ensures that everything is written to the disk and properly saved before turning off.

For iCloud stored data, everything is stored locally on your own disk first - and only synced to iCloud later (although "later" could be a split second later).

In total: If you have experienced data loss, it wasn't because you shut down the Mac. It is either a case of (a) you have actually saved the data, but can't find it, or (b) a mal-functioning program.

If you have Time Machine backups set up, you might be able to find a recent copy of your project in the backup.