One can simplify further I think[^1], removing a redundancy:

local looking_at_section = false
local lvl = 0
local remove = {}  -- delete line if 'remove' array not needed

function Block (elem)
  if elem.t == "Header" then
    -- if elem.classes:includes('remove',1) then
    if elem.identifier == 'remove' then
      looking_at_section = true
      lvl = elem.level
    else
      looking_at_section = looking_at_section and elem.level > lvl
    end
  end
  if looking_at_section then
    remove[#remove + 1] = elem  -- delete line if 'remove' array not needed
    return {}
  end
end

Note that in the original "abstract" script example, the removed portion was recreated as a meta section. If you don't intend to use the removed elements, you can simplify further (as noted) by removing the two lines related to the remove{} array.

[^1]: As long as the filter acts from top to bottom of document among the Blocks, i.e. if there's no unknown precedence rules among all the Block types... which I'm not 100% sure.