I was trying to get platinum trophy at the game, but several comics and training manuals dont show at the suposed place they belong. Dont know how to make them reapper. I got these specific missing colectibles at an early "new game" but they don't show in the story nor in the chapter tracking list.
If you're on New Game Plus; any previously picked up training manual does not show up again. Comics, pendants and artifacts on the other hand shouldn't disappear.
My best guess is that you've got a glitched save file. Try restarting the chapter you're on (main menu -> tlou -> chapters) and make a new save file.
.....and/or you keep your ps4 in rest mode a lot (or are you on ps3?), i.e. not turning it off fully often enough. I know from experience that can cause weird behavior in some games. If so, power cycle your system and then load up the game again and/or restart the chapter and make a new save file as well.
If the above doesn't work, delete the game and reinstall it.