Python flask with multi modules application OperationalError: (sqlite3.OperationalError) no such table

I have been learning python recently and practiced a couple of tutorials and its been going fine, till I have divided my application to sub modules to make it easier to maintain using blueprints, after doing so the application crashed and throw the following error: OperationalError: (sqlite3.OperationalError) no such table, here is how im dividing my application:

-instance
  -flask.cfg
-app
  - static  // Folder for css
  - templates // Folder for common html files
  -__init__.py // to init the app 
  -module1
    -__init__.py // to register module blueprint
    -subModule1
      -subModule1 Group1
        -templates
          -htmls files
        -__init__.py file //to register group1 blueprint
        -Group1Form
        -Group1Model
        -Group1View
      -subModule1 Group2
        -templates
          -htmls files
        -__init__.py file //to register group2 blueprint
        -Group2Form
        -Group2Model
        -Group2View
    -subModule2
        ....
-main.py

The application run fine when I use flask run but I have an issue when I use db.session.add() method with the exception that the table was not found. I have tried many solutions to this issue but no luck. here is some links for the same issue:

OperationalError: (sqlite3.OperationalError) no such table: user

https://flask-sqlalchemy.palletsprojects.com/en/2.x/quickstart/

Python sqlite3.OperationalError: no such table:

'No application found. Either work inside a view function or push an application context.'

Here is the flask.cfg file:

import os

BASEDIR = os.path.abspath(os.path.dirname(__file__))
SECRET_KEY = os.urandom(32)
DEBUG = True
SQLALCHEMY_DATABASE_URI = 'sqlite:///' + os.path.abspath('app.db')

And here is how I am initializing the app in the main __init__.py file:

from flask import Flask
from flask_sqlalchemy import SQLAlchemy

db = SQLAlchemy()

def create_app(config_filename=None):
    app = Flask(__name__, instance_relative_config=True)
    app.config.from_pyfile(config_filename)
    initialize_extensions(app)
    register_blueprints(app)

def create_app(config_filename=None):
    app = Flask(__name__, instance_relative_config=True)
    app.config.from_pyfile(config_filename)
    initialize_extensions(app)
    register_blueprints(app)
    return app

def initialize_extensions(app):
    db.init_app(app)
    with app.app_context():
        db.create_all()

def register_blueprints(app):
    from app.module1.config.university import university_blueprint
    app.register_blueprint(university_blueprint)

    from app.module1.config.department import department_blueprint
    app.register_blueprint(department_blueprint)

    from app.module1.authors.author import author_blueprint
    app.register_blueprint(author_blueprint)

    from app.module1.authors.publications import    publications_blueprint
    app.register_blueprint(publications_blueprint)