I don't know whats the problem with my main quest items, since I'm picking up the elements of Ancaria I don't see them in my backpack, I alredy picked up the air and fire elements and other items from secondary missions and they don't appear as well.
This never happened to me before, and I'm not sure if I can keep going like this or if I need to start again exporting my character.

Quest items don't generally appear in your backpack inventory (exception: the whiskey barrel smuggler quest). But they should appear in your quest log - as you collect quest items it gets recorded in the quest description itself, and certain collected items also get listed on a special tab in the log as well.

As long as you see yellow main-quest icons on the map, you are doing fine. But you have to collect the Elements of Ancaria in the proper order (Air, Fire, Earth, Water) or you will encounter a main-quest bug when it is time to bring the elements to Shariffa where no more yellow icons are displayed. If you get this bug, it is recoverable w/o needing a restart.