Hello linguistian,
CEP2 writes a big result file which takes a long time to upload. This means that the check points can also be gigantic. There are 16 jobs, so-called, in a task. Each is a different algorithm running over the task. Therefore there are 15 checkpoints written between jobs. The most important information comes first. The last is optional for any particular task, although the information is wanted for a percentage of the adjacent tasks. There is no solution for the loss of computation time within a job. If you reboot during Job #2, the longest one, you may lose several hours. You can see in BOINC Manager how long it has been since the last check point by selecting the CEP2 task and clicking on Properties, which lists some information. Since I only reboot for a reason, I prefer to ignore CEP2, since it always hurts if I lose more than a few minutes.

Lawrence