Flask - One flash message will not go away, due to functools.wraps?

I am building a simple flask webapp as part of Harvard's CS50 Web Programming Course to learn web development. I've successfully got user registration / log in / logout implemented, along with various message flashing to give the user feedback.

For some reason, the "Login Successful" flash message just won't go away after its displayed. I've read the documentation, and some useful posts like this and this. It seems like any route with the @login_required decorator can't get rid of the flashed message.

Fully working code is here: GoodBookBadBook

Here is the application.py file:

import os
from flask import Flask, session, request, render_template, url_for, redirect, flash
from flask_session import Session
from sqlalchemy import create_engine
from sqlalchemy.orm import scoped_session, sessionmaker
from werkzeug.security import generate_password_hash, check_password_hash
import functools

app = Flask(__name__)

DATABASE_URL = "postgres://xqmbmqkcvpavvs:17f6f6f690bb777e4d484e3ee441e3b4d8c88591d239a9beb49aca4599863b97@ec2-52-70-15-120.compute-1.amazonaws.com:5432/dfg72kp1ckutig"
app.config["DATABASE_URL"] = DATABASE_URL

# Configure session to use filesystem
app.config["SESSION_PERMANENT"] = False
app.config["SESSION_TYPE"] = "filesystem"
Session(app)

# Set up database
engine = create_engine(DATABASE_URL)
db = scoped_session(sessionmaker(bind=engine))


def login_required(route_func):
    @functools.wraps(route_func)  # returns wrapper as route_func (?).
    def wrapper(*args, **kwargs):
        print(f"wrapper flashes: {session.get('_flashes', [])}", flush=True)
        if "logged_in" in session:
            return route_func(*args, **kwargs)
        else:
            flash("You must log in to use GoodBookBadBook.", category="error")
            return redirect(url_for('login'))
    return wrapper


@app.route("/")
def index():
    print(f"index flashes: {session.get('_flashes', [])}", flush=True)
    return render_template("index.html", logged_in=session.get("logged_in", False))


@app.route("/main")
@login_required
def main():
    print(f"main flashes: {session.get('_flashes', [])}", flush=True)
    return render_template("main.html", logged_in=session.get("logged_in", False))


@app.route("/books")
@login_required  # calls wrapper() with arguments to books().
def books():
    print(f"books flashes: {session.get('_flashes', [])}", flush=True)
    books = db.execute("SELECT * from Books").fetchall()
    return render_template("books.html", books=books, logged_in=session.get("logged_in", False))


@app.route("/books/<int:book_id>")
@login_required  # calls wrapper() with arguments to books().
def book(book_id):
    print(f"book flashes: {session.get('_flashes', [])}", flush=True)
    book = db.execute("SELECT * from Books WHERE id = :book_id", {"book_id": book_id}).fetchone()
    print(f"book() /books/book_id {book}", flush=True)
    return render_template("book.html", book=book, logged_in=session.get("logged_in", False))


@app.route("/authors")
@login_required  # calls wrapper() with arguments to authors().
def authors():
    print(f"authors flashes: {session.get('_flashes', [])}", flush=True)
    books = db.execute("SELECT * from Books").fetchall()
    return render_template("authors.html", books=books, logged_in=session.get("logged_in", False))


@app.route("/signup", methods=["GET", "POST"])
def signup():
    username = request.form.get("username")
    pwd = request.form.get("pwd")
    repeat_pwd = request.form.get("repeat_pwd")
    print(f"signup flashes: {session.get('_flashes', [])}", flush=True)
    if request.method == "POST":
        if validate_registration(username, pwd, repeat_pwd):
            hash = generate_password_hash(pwd)
            db.execute("INSERT INTO Users(Username, Hash) VALUES (:username, :hash)",
                       {"username": username, "hash": hash})
            db.commit()
            flash("Registration successful.", category="success")
            return redirect(url_for('login'))
    return render_template("signup.html")


def validate_registration(username, pwd, repeat_pwd):
    existing_user = db.execute("SELECT * from Users WHERE Username = :username",
                               {"username": username}).fetchone()
    print(f"validate_registration flashes: {session.get('_flashes', [])}", flush=True)
    if existing_user:
        flash("Username unavailable.", category="error")
        return False
    if len(username) < 3:
        flash("Username must be at least 3 characters", category="error")
        return False
    if pwd != repeat_pwd:
        flash("Passwords do not match.", category="error")
        return False
    if len(pwd) < 3:
        flash("Password must be at least 3 characters.", category="error")
        return False
    return True


@app.route("/login", methods=["GET", "POST"])
def login():
    username = request.form.get("username")
    pwd = request.form.get("pwd")
    print(f"login flashes: {session.get('_flashes', [])}", flush=True)
    if request.method == "POST":
        existing_user = db.execute("SELECT * from Users WHERE Username = :username",
                                   {"username": username}).fetchone()
        if not existing_user:
            flash("No user found. Please sign up first.", category="error")
            return redirect(url_for('signup'))
        if not check_password_hash(existing_user.hash, pwd):
            flash("Incorrect password.", category="error")
            return
        else:
            session["logged_in"] = True
            flash("Login successful. Thank you for using GoodBookBadBook.", category="success")
            return redirect(url_for('main'))
    return render_template("login.html")


@app.route("/logout")
def logout():
    print(f"logout flashes: {session.get('_flashes', [])}", flush=True)
    session.pop("logged_in", None)
    flash("You have successfully been logged out. Come back soon!", category="success")
    return render_template("logout.html", logged_in=session.get("logged_in", False))

Been stuck on this all day, any help is appreciated.

EDIT: I updated the git repo to remove all references to a timeout script. I am not going to use a timeout script in the final code.

EDIT 2: Here's a 30 second video of the problem.