If you decide to discard a prepared skill card for your role (such as guardian 1) during the rally step do you get to prepare it again for the next action step or is it shuffled back into the skill deck?

The Rally Phase is the last phase of each round (after Action and Shadow), and you reset (reshuffle) your deck before you scout and prepare. So if a card is discarded during the rally phase (I assume as a result of having the maximum of four cards prepared?), it will sit in the discard pile for the following action and shadow phase, until the next rally phase.

No not discarded during rally. For example I have to prepare guardian 1 at the start as per the rules. On my turn I use that card to prevent damage. When I reset do I get to prepare that card again or does it get shuffled back in the deck and prepare a new skill card that a draw during scout? Also are items considered towards the prepare limit of 4? Sorry I should have explained a bit better

Yep. If you use your starting skill card, it get sufled in the deck with the rest and you may later prepare is it you happen to draw it while scouting.

items Are not skill cards so no... They have their own rules of limitations.

If you discard your starting role-specific skill card, it is not automatically re-prepared it when you shuffle your deck. You'd have to prepare it while scouting to get it again.

Items are not counted toward you're limit of four skill cards. So you could have an armor card, two hands' worth of weapons, one trinket at the start of the adventure, anymore you discover in that adventure, max one of each boon, and four prepared skills.

One more card type is boons and They neither affect to you prepared skill cards.

Cool thanks