Tanvi;
Not sure I fully follow the question, but the main issue appears to be when deleting a thermal zone the space disappears, yes? A key understanding within eQuest/DOE is that thermal zones __are__ spaces; this is different than OpenStudio where there can be multiple spaces assigned to a thermal zone. While they are defined separately in the input; zones & spaces have a 1-to-1 relationship within eQuest.
Backing up, I would question first if these zones actually need to be deleted. If their 'unconditioned' then set them to 'unconditioned' and move them to a nearby HVAC system. They wont receive any conditioning (being unconditioned), but the thermal zone will still transfer heat to/from adjacent zones. Any concerns about extra/fake/non-existent plenums may be overblown. If its an unconditioned zone with an unconditioned plenum, set them to unconditioned & be done with it. Can change the ceiling construction to 'air wall' if concerned about any temperature delta between the two or other adjacent zones.
Extensive geometry modifications post-wizard is not for the faint of heart; polygon modifications are hard & I advocate avoid if at all possible. It's tedious and can corrupt a model if done wrong. This is not wall height or floor-to-floor, thats straightforward enough.
Let us know if this is/was the right understanding of the question.
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