I have more screenshots still sitting on my PS4, which I will put up later. I've also added updated screenshots for some previous chests including ones that didn't spawn for me on previous runs.
Chest #1 - Screenshot of chest before loot ninjas got to it.
Chest #3 - Screenshot of chest.
Chest #4 - Chest spawned on another run.
Chest #7 - New location near Chest #5 (Thorn always getting in the way XD)
Chest #4 - Right at the end of the mission after you beat the final boss and are heading to your ship.
Chest #5 - After you complete the first defense objective. Climb back up onto the conveyer belts and follow it outside to some platforms. There's a second platform that seems to require a character that can jump pretty well (although I saw an ISIC somehow make it over there which is how I discovered it in the first place). Will add more screenshot steps next time I play this mission.
Chest #2 - Updated screenshot of chest spawned.
Chest #9 - Updated screenshots of chest spawned.
Chest #4 - At the bottom of a small waterfall in the first section you have to defend S1.Chronicle.
Chest #5 - Near Chest #3's location at the base of a ledge.
Chest #6 - Actually don't remember this one. Will update a description later.
Chest #7 - Right before you start the boss fight. A bunch of Thrall will spawn right in front of it.
Chest #8 - Another one I can't remember.
Chest #9 - Inside an alcove (has a fairy fountain vibe) to the right of where Mellka is preparing the Data Minion (thingies).
Chest #10 - Underneath the middle area of the Data Courier section where all the Varelsi spawn.
Chest #11 - This one is also near the end of the escort section.
Chest #1 - Behind the 3rd defense objective area (where you are uploading data with wooden WiFi)
Chest #2 - Another fairy fountain type area that will likely only go near during the final boss fight.
Chest #3 - To the far left of the the second defense objective on top of a Temple of Time like platform. An MX.Super Elite (Toddler) bot generally spawns around here during the clean up phase before the defense objective starts. Again sort of out of the way, hence why it can be easily missed.
Chest #4 - Supervisor Antem has 3 spots he jumps back and forth to. This chest is located at the middle location.
This mission has a lot of puzzley platform type secret areas and I also forgot to screenshot how I got to some of these >_>
Also I really love how these loot chests are hidden and I hope there are more like this in future story missions!!
Chest #1 - Behind a shard barrier and requires climbing over the top to get to on your way to Guardian Vyn. This one requires jumping onto the last Spike platform from the stairs and falling into this area from the top. Will update this the next time I play the mission.
Chest #2 - Also behind a shard barrier found on your way to Guardian Arc. This one requires running past this point, jumping on top of the Spike Platform as you head out into an open area where heaps of Thrall spawn, (you need to run around the edge of the circular hill to get on top of the Spike platform) and then falling through the hole in the top.
Chest #3 - On your way back from beating Guardian Arc, you can either fall through a hole or back through the area with lots of Spike platforms. If you keep jumping across these to the last one you will find a hidden alcove with a share generator that powers the shard barrier you will have seen on your way to the mini boss.