Another interesting bit about the checkpointing, any time the game saves during an encounter, it will save your time in that encounter and if you've taken damage. So if you happen to call Courtney and save after you have taken damage or have wasted time in an encounter (remember, some encounters start the clock as soon as you enter the room, even if you haven't attacked an enemy or been spotted yet), you might screw yourself out of being able to get the S rank on a restart.
But what is especially interesting, is that this applies any time the save logo appears on your screen for any reason. So if you happen to collect a Left Arm, or a Data Chip, it will save your current time and whether you have taken damage. Luckily, this will pretty much never happen again once you have all of the collectibles (unless there is some other condition for auto-save I am forgetting), but it is a potential problem if you are trying to get collectibles and S ranks in the same playthrough (like I am).