Delete an entry from many-to-many relation

I have encountered these kind of issues so many times now.
You should not query the model, it doesn’t work, I have no idea why.
What you should do instead, is querying the DB directly.

qb.from("builds_users__users_builds");: what you are doing here is querying a Bookshelf model using Knex syntax

What you could try to do is querying the DB using Knex directly:

const knex = strapi.connections.default;

Then something like

//you should check out knex docs
const res = knex('build')
     .join("builds_users__users_builds")
        .where("user_id", "user.id");
        .andWhere("build_id", "in", function(qb) {
          qb.select("id").from("builds")
            .whereIn("folder", function(qb) {
             qb.select("id")
                .from("folders")
                .where("project", "project.id");
            });
        });

I am honestly very disappointed by this ORM

Anyway, this WHERE project = ${project.id} is not the way it should be done. This is subjected to sql injection attacks.

It should be like this ( according to knex’s documentation):

WHERE project = ?" ), project.id)