Missing First 2 Atlas Points

I beat the first nexus and used the item. i briefly saw the you have 2 points icon about my xp bar.

i opened a portal and clicked it (i planned to deal with them when i got out) and now theyre gone and im missing the item :(

my atlas tree says 0/40 and i cant use the refund function or anything (i was just trying stuff because why not)

help me ggg, youre my only hope

EDIT: it is worth noting i couldnt log back onto that character from login until i restarted the game. before i restarted i could still log into other characters. i would have been portaling back to the ziggurat basement place