Early on in Avengers: Endgame when Ant-Man/Scott Lang is attempting to explain the quantum realm and also how the supply of Pym particles is limited...
...since Hank was dusted during the mid-credit scene in Ant-Man and the Wasp.
He proceeded to state there were enough Pym particles for two trips each AND two tests... where he proceeded to waste one "test", Hawkeye/Ronin volunteered to test the time travel concept.
All this worked, permitting the main mission to go ahead:
All Avengers were given a vial with enough Pym particles to jump to their designated time-space AND return. Captain America and Iron Man had to take an additional jump to the 70's due to the Hulk incident in securing the Space Stone. Since Dr Pym and the Tesseract were in the same place at the same time, they could collect enough Pym particles to make the return jump.
However... halfway through the film
when past-Nebula's memory started to be populated by "present"-Nebula's memory and Past-Thanos/Nebula captured "Present"-Nebula on Morag while they planned to take the Power Stone before past-Star-Lord steals it, the past-Nebula took "Present"-Nebula's quantum GPS and the remaining ONE-JUMP Pym particles. She used this last batch of Pym particles to jump to the new present.
So if all the stock was used up
what Pym particles were used to transport Thanos's ship into the Quantum realm and equally what quantum GPS was used if Past-Nebula needed to use both?