Thanks @posertinlab and @alburse, that makes more sense to me now.
In my case, I had run an extract job with ~3.5m particles and I was indeed hoping to split them up in smaller batches using the Particle Sets Tool. Simply splitting the particle stack into smaller batches did not reduce the particle stack size to fit on the SSD, however, I am able to run an Ab-Initio job telling it to only use 300k particles (from the 3.5m stack) and it runs fine on the SSD. This makes me think it should be possible to have an option in the Particle Sets Tool to ‘truly’ split the particle stack, rather than having to re-extract and use up more disk space?
Maybe someone on the CryoSPARC @team can comment on this possibility?