Yhyjyk

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 vile 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... half way 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?

The plan was to re-shrink the Benatar on Morag and bring it back to Avenger's HQ when the Soul Stone had been recovered.

Rocket: You promised to bring that [The Benatar] back in one piece.

Clint: Yeah yeah yeah yeah. Ok, do my best.

Since we don't see the ship again until much later (after the battle), it's possible that Clint, in his distressed state, used his personal particle to jump straight back to present-day Earth and left the Benatar on Vormir for Thanos to find, along with its remaining Pym particle (presumably housed in one of Ant Man's shrinking disks).

Thanos definitely knew the location of the Soul Stone (courtesy of FutureNebula's memories) and would have been in the vicinity of Vormir at some point shortly afterward, found the abandoned Benatar parked near to the temple, realised what the disk contained (again, courtesy of stolen memories) and then used the particle to shrink his own battleship when PastNebula contacted him from the future. Since the Guardian's ship had no other value to him, he probably would have just left it on the planet, as junk, for Captain Marvel to later collect and bring back to Earth.

Past Nebula uses the time machine constructed by Professor Hulk to bring Thanos’ ship into the future.

I don’t think we see exactly how, but she may be using spare Pym particles brought back by Captain America (he does, if I remember correctly, steal three vials from 1970, when he and Tony presumably only needed one each). She definitely seems to use Pym particles when bringing Thanos’ ship forward, as we see the ship increasing in size as it exits the Quantum Realm.

To add another theory into the mix I think it is quite possible that since 2014 Nebula had stolen the Pym particles from 2023 Nebula that she showed them to Thanos. Once he was in control of them anyone under his command would have been able to access them as he wished and seeing as humans are apparently not that smart, as Rocket says to Tony, then one of his people could have recreated the Pym particle. Once recreated they would have had enough of a supply to be able to bring the ship and everyone on it to 2023.

I think this makes more sense as they would likely need more than one vial to bring all of that into the future, otherwise the team would have traveled to 2014 in the Benatar rather than shrinking it and carrying it in their pockets and then they would have had more than enough vials rather than just the right amount.