Yes, you can remove it manually in the json file. Though it will not achieve what you want.
The part you're looking at is actually the fixtures section, which the plugin does not use at all when placing furniture.
Wait, no. The Fixtures thing on the JSON is like the floor, wall, and lighting aspects. I didn't mean that.
The part I'm looking at is "interiorFurniture": [
Here is an example one.
{
"attachments": [],
"name": "Admiral Portrait",
"itemId": 7095,
"transform":
{
"location": [ -152.74824523925781, 198.90545654296875, 171.87091064453125 ],
"rotation": [ -0, 0, -0.70722877979278564, 0.7069847583770752 ],
"scale": [ 1, 1, 1 ]
},
"properties": []
},
This is the Admiral Portrait hung on a wall in my House on the Basement level. If that is the only piece of furniture on the basement level and I totally delete that line in the JSON, when I load the JSON with the plugin, only the ground floor (of the Small) should be altered or adjusted.
Not saying it wouldn't be a bit of a pain in the ass, of course. But I think using a few in-game coordinates could help to work out what was where for quicker removal. Using XZ to determine what number is used for the far left/right chambers, and Y would help to govern the floors.