Since no one answered I worked on it till I came to a somewhat simplistic solution that works, although it's not perfectly dynamic as you will see later.
All the dynamically generated items have ids like f02_0000 where the 02 is the idx of the item and the 0000 is the row(the first item it generates is 0000, the second is 0001,...)
I made a bunch of hidden items on the page and the same number of application items, and named them all in sequence(ITEM_1, ITEM2,...)
Then I made a Dynamic Action on the page, Event : Change, Selection Type: jQuery Selector, jQuery Selector: input[name = "f02"] --all the apex_items you enter are p_idx => 2 in my scenario.
This DA has a Javascript action that gets the number of the triggering element with
parseInt(this.triggeringElement.id[this.triggeringElement.id.length -1])
This of course only gets the last number of the id, but changing this is easy.
Then I also have an action here that assigns the value of the page item to its corresponding application item.
:APPLICATION_ITEM_1 := :ITEM_1;
Where I also put all the items into Items to Submit
And then I change all the LOVs to use the corresponding application items.
I did some extra things like clearing all the page and application items on refresh and such, but you can play around with this.
This works, but its a bit of a dirty solution as you need to make it work for however items you generate. So if you know you will only generate up to a certain amount of items, this will be fine, if it can go up to a ridiculous amount of items, then you need a different solution.