SQLAlchemy - Closing Session Blocks Code Execution

I have a query that runs as a batch using SQLAlchemy yield_per. This is a long duration query and I wanted to have a time limit for how long I run this query for. When the time limit is crossed I close the SQLAlchemy Session and break out of the for. The code gets stuck at the session.close statement after raising the following warning -

/Users/user/opt/miniconda3/envs/project/lib/python3.6/site-packages/pymysql/connections.py:799: UserWarning: Previous unbuffered result was left incomplete warnings.warn("Previous unbuffered result was left incomplete")

Below you can find a simple recreation of the code.

class QueryExec:
    def __init__(self, uri, connect_timeout, statement_timeout, pool_size, max_overflow) -> None:
        try:
            self.engine = create_engine(
                uri, #PyMySQL Driver is used.
                connect_args={
                    "connect_timeout": connect_timeout,
                    "read_timeout": statement_timeout,
                    "write_timeout": statement_timeout,
                },
                pool_size=pool_size,
                max_overflow=max_overflow,
            )
        except Exception as e:
            exit("Exiting as we couldn't connect to database")
        
    def execute(self, batch_size):
        start = datetime.now()
        
        #Create Session
        session_factory = sessionmaker(bind=self.engine)
        Session = scoped_session(session_factory)
        session = Session()

        query = (
            session.query(Table)
            .with_entities(
                Table.Row1,
                Table.Row2,
                Table.Row3,
            )
            .order_by(Table.Row3.asc())
            .execution_options(yield_per=batch_size)
        )
        
        for query_results in session.execute(query).partitions(batch_size):
            # Perform Operations on query_results for every batch

            # After every batch check -
            time_since_start = datetime.now() - start
            if time_since_start>timedelta(hours=1):
                session.close() # Gets stuck here
                break

        return

I am still figuring out how to work with SQLAlchemy, could someone help me with how to continue code execution after session close. Thanks!