I suggest using hibernate rather than shutdown.
You may need to enable this from Control Panel, Power Options.

CEP tasks are very long running and can have long periods between checkpoints, hence much lost time.
Others checkpoint more often so less time lost.

Paul.

If you have to shut down your computer at night then CEP2 may not be a good project for you.

The longest jobs in a task are first one and last one, second to penultimate ones last about 20 minutes (at least in my case): if you see that the last checkpoint happened more than 20 minutes ago it means it's performing the last job and you have to wait until it's done to shut down to avoid losing a notable period of work.

It's not necessarily true that this project is suitable for 24/7 crunching only since you can observe the runtime fo WUs and find out how it depends on the size of the molecules (just look at the number of carbon atoms in the name of the WU) then esteem how many WUs you can complete during the period your PC is operative.
If you can't or don't want to do this brief check when you start Boinc Manager then CEP phase 2 is suitable for 24/7 crunching only.

Don't forget CEP phase 2 is an opt in project precisely to avoid people wasting their resources: if you have to attach to it on purpose it's obvious you should take a look at the information about it (FAQ, forward on CEP site or WCG site) before starting to crunch. If you do so you'll immediately learn that it's a tough project and won't even start it or you'll start it expecting it could be unsuitable for you and once you've proved thath you'll quit it.