In this thread you can find all checkpoint restarts that you can do during a run. There are at least a few more out there, but they are not as useful and barely save you any time. I will cut this in 2 posts: ch1-ch6, ch7-misc.

ch1: After you done with walking section you have to crouch and go through the grate. Once you lose control of Chloe and she starts to open the grate by herself - game autosaves; if you restart checkpoint here - it will put you around the corner, making you skip animation of her moving the grate and walking a few steps: ~7.5s timesave

You can save ~2s here: once Chloe says word "Pink" in this cutscene - reload a checkpoint - which will make you skip her putting away phone and allow you to walk right away.

ch2: Antique shop: once Chloe starts to raise her hand up - you can pause and notice that game autosaves - restart checkpoint here. It will allow you to skip ~5.5s of cutscene. Note: be careful with that reload, because it's very easy to pause it too early - just take a look at "Autosaving ... " message in pause - if you see it, then your timing is right.

ch4: When you managed to pull down this gate you will hear a loud noise - that's when you can restart checkpoint to spawn closer to the entry and save ~4.5s.

ch5: If you are fast enough in this climbing section you will have to wait ~8s for Nadine to give you a hand - reloading a checkpoint once you grabbed last ledge will spawn her next to you immediately.

If you are not doing APC skip, you have 3 ways to go around the fight. One of those is to jump over those pink-ish plants into the dirt - if you jumped correctly - the game will autosave; reloading a checkpont will place you closer to the wall you need to climb.

Once you climbed on this wall - restart checkpoint, it will teleport both Nadine and You closer to the door infront of you.

You can reload the checkpoint right after you reached on of the ledges of this wall (reference screenshot) - it will allow you to skip ~3.5s of climbing and watching animation of falling down AND will put you directly into cinematic.

ch6: During the dirtslide: as soon as you lose control of Chloe, you can restart checkpoint to appear a bit further ahead. That allows you to skip animation of Chloe finishing the slide & standing up, saving you ~8.5-9s (props to @Mattmatt for the find)

After meeting elephant family: once you climb this ledge and Chloe will start talking - game autosaves, and reloading it will put you a further in the area, saving you ~6s of jump-rolling.

ch7: Right before the room with a giant tusk - you can reload a checkpoint when you passed the 2nd octagon on the floor - this will teleport Nadine closer to you, because you need her be available asap to checkout the tusk.

ch8: in the beginning of the chapter you can reload a checkpoint while sliding down the dirt and appear further in the area, saving ~3.5s. Technically, you can jump right into that trigger, but there is a big chance that you will die from fall damage.

Once Sam made his jump and you regained control of Chloe AND made at least one step forward - you can see game autosaving; reloading will put you a bit closer to the wall you need to reach, saving you ~2s.

Section where Chloe has to wait for something to grapple to has an autosave, that happens when you grab this long ledge AND Sam started to say "By the radio tower. Nadine, do you see a way up?". Restarting will save you whooping ~14.5s - teleporting you on higher ledge and skipping the wait for Sam and Nadine.

While waiting for Sam, there is a checkpoint restart that you can do - just look at Nadine's flashlight - once it's turned ON you can restart. This will teleport you on the other side and skip ~31s of dialogue.

Once you grappled to the helicopter - you can restart checkpoint and get a bit higher on the rope that way - timesave of ~3s.

ch9: To save ~8s, spawn 4x4 faster and closer to you - you can reload a checkpoint after you jump into this wagon from a rope.

Once you done driving first 4x4 - you have to jump on a platform. Waiting for next 4x4 and a truck with turret will be a huge waste of time - so going into next wagon, triggering "Blocked Again" phrase and restarting a checkpoint will allow you to spawn everything closer to you.

Last reload is happening once you have killed all Asav's men who interrupted you from changing tracks. Reloading will put You closer to the lever, and train - closer to you.

Miscellaneous: This restart may or may not be needed. While moving to the 3rd mirror Chloe must say "Got it" phrase; if she doesn't - then you have to restart checkpoint after Nadine takes 3rd mirror from you.

This restart is purely optional and very handy if you having problems emerging from the water while dodging falling rocks. Once Nadine and Sam start going up and you regain control of Chloe - game autosaves, and you can restart checkpoint. It will spawn you in the same place, but - holding X (to swim up) here will make game guide you in a perfect line to dodge all rocks. You don't need to do any inputs other than holding X throughout whole section. Loses ~0.5s, but guarantees to not lose 9s.