In order to make time for writing I must give up working or gaming...
1. When enemies are discarded because they are defeated they go to a discard pile. When drawing a new encounter and you draw enemies that do not match encounter keyword, are they discarded into the same pile as for defeated enemies?
Yes they are.
3. Could you potentially rest twice in a turn...once in hero phase if no enemies and it's safe and then during encounter phase from aftermath?.
No. If there is no Active Encounter (ie. you finished it last turn and you haven't drawn a new one) you don't get an Encounter Aftermath Phase.
4. Time track:
-why are there empty spaces to the left of the 1 hero marker
I think the designer originally intended for there to be effects that could buy you back Time (moving the time cube leftwards) but this idea didn't appear in the final game, but the time charter preserves that idea. Just ignore those spaces.
-does the rage symbol above the number 2 (white number on black background) mean anything?
-what does the very first square mean (shows plus 1 resolve, move time track right 2 places)?
As above, ignore those spaces. They seem to be legacies of some earlier iteration of the rules. They don't feature at all in the new Time Charter for Heart of the Mists.