"Let's try to sort this through chronologically...
Of the ship memories, the fleet one is obviously the first, being the field test. Then either the burning world or embedded globe, followed by the other. Then the cheering keyboard, then the empty void.
The individual memories are trickier, since they're likely from different individuals, but it should start with the drifting helmet, and indeterminate order of the syringe zeppelin, the nerve node, and the metal bench, finally going into the hiding face.
Hang on... during the embedded globe memory, the ghost ship was feeling elated at destroying an Altered ship. The feeling of kinship and sadness from the field test then aren't likely to be for the Altered. Either the emotions are what the ship thought at the time, and at the time it was indoctrinated as 'save humanity, kill Altered'. Or they're what the ship feels now, and it is still elated that it destroyed that Altered ship. A feeling of 'An enemy destroyed' in the embedded globe. Being told that 'there were humans on the planets, perhaps there are still humans on the planet as well, but they're being killed, dying, and we need to kill the enemy' would explain the feelings of kinship and sadness.
Okay, strike the field test and embedded globe, strike the empty void as secondary. Strike the drifting helmet as reinforcing the view of the Altered as enemies, Strike the metal bench as reinforcing the... preferable world view. Leaves burning world, keyboard, syringe zeppelin, nerve node, and hiding face....
You know, I've known a guy with a dog, who didn't treat the dog very well. The dog got yelled at a lot, for the least of things, sent out of sight, got less food than was probably good, and was generally treated as a thing... and while the dog always liked to meet other people, get a few scraps off them... the dog still loved its master dearly, would be sad if left alone by him for a while..."