Since skript doesn't allow for you to save specific inventories, you have to save the specific items inside of the inventory as a variable instead. Something like this should work:

Code (Text):

1. command /backpack2:
2.     permission: op
3.     trigger:
4.         if {backpack::%uuid of player%::*} is set:
5.             open chest with 3 rows named "&8Backpack &7- &b%player%" to player
6.             set player's current inventory to {backpack::%uuid of player%::*}
7.             delete {backpack::%uuid of player%::*}
8.             stop
9.         open chest with 3 rows named "&8Backpack &7- &b%player%" to player
10.        
11. on inventory close:
12.     if name of event-inventory is "&8Backpack &7- &b%player%":
13.         loop all items in event-inventory:
14.             add loop-value to {backpack::%uuid of player%::*}

 

If i'm correct, arrays don't exist in skript. instead there are lists: {list::*}. You can set individual index of the list like this: set {list::5} to 5.