Good morning,

A question: If someone creates a [WIP] mod based on another mod that has permission or is freely usable, and the original mod is voluntarily deleted, will the mod in progress also be deleted?

Greetings!

If it's based on a Creative Commons license, then these licenses are irrevokable. So if a mod have been released as CC-BY then removing the mod doesn't void the license and you can still make derivs of that mod.