Every time I start my server up, the config file resets. I just want to keep delete items on false but it never remains that way.

please post the version are using, server version and other plugins installed.

I can confirm I get the same behavior.
Version: 5.4.0
Server: git-Spigot-988b411-1f4693a (MC: 1.16.3) (Implementing API version 1.16.3-R0.1-SNAPSHOT)
Other plugins: (all latest versions at the time of writing)

• Death coordinates
• Fast leaf decay
• GtzDoors
• LuckPerms
• Minepacks
• Simple player tracker
• Set homes
• Silkspawners
• Single player sleep 2
• Timber plugin
• Twerktree
• Vein miner

I am unable to reproduce this.

closing for this for now as I cant reproduce this and no info has been provided, if more info is provided this can be reopened