Several tools exist to work on minecraft worlds to clean out blocks. If you remove blocks and chunks, then more new ones will spawn with the juicy goodness of world changes and latest updates from MC.
Get the latest MCA Selector
https://github.com/Querz/mcaselector
Get the latest buildtools installed
https://www.spigotmc.org/wiki/buildtools/#windows (requires git and latest openjdk)
https://adoptium.net/temurin/releases?version=17 - Change to the right version, select for Windows
https://hub.spigotmc.org/jenkins/job/BuildTools/lastSuccessfulBuild/artifact/target/BuildTools.jar
Copy it to C:\minecraft_server\build_tools
Run update_and_run_BuildTools.bat
Copy world, world_nether, and world_end into a backup folder.
Stop Services for Minecraft.
Run MCA Selector.
Update BungeeCord
https://ci.md-5.net/job/BungeeCord/
Change run.bat for spigot_survival to the newer version.
Start Services for Minecraft.
To troubleshoot, run watch_logs.bat, or stop the service and launch it again in the current user run.bat instead.
Clean up plugins, or update plugins if you are a glutton for punishment.
for MC <1.11 MCEdit was the standard.
http://www.mcedit.net/ Last update in 2016.09
MCEdit was superceded by Amulet.
NBTExplorer gets some mentions
WorldEdit is a popular spigot plugin for terraforming and importing/exporting schematics in game.
And if you aren't really editing, but just removing chunks, then MCA Selector sounds like the way to go.
See the fourth comment on this page:
https://gaming.stackexchange.com/a/27623/274559