"Or more easy, i don't know if this can be done, just save the game, all countdowns are paused, when you open the game again the countdowns are unpaused but subtract the away time to all countdowns"
That is the way to go. rex_time_awayL don't care about object, array or any other stuff it simply saves the key (you set the name) and value (time)
1. You don't array but you can use if your enemies have some stuff to save (like position, variables, states etc or even respawn time) then Array will help organizing it
2. If you set proper naming convention for Time Away then yeah. It's a matter of simple for each loop
Countdowns don't need to run every tick. You can update them ever 1 second, and don't worry about the lag. I have a mobile game where I have very similar setup
and on my old Samsung Galaxy S3 it checks an array with 900 items every one second and it's perfectly fine.
But just in case I've modify my system a bit. At start array is empty (size 0,4,1) every time enemy is destroyed I'm adding a new index to the array, and when enemy is respawn I'm removing it, It reduced the countdown checks from 900 to max 20-30 a second