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Yes, engine.execute is deprecated in SQLAlchemy itself. You don't need to create a session (and can't after #1087 makes those setup methods private), you should just do db.session.execute. #1087 makes the engines available in the db.engines dict mapping bind keys to engines.
flask-sqlalchemy support multiple connections through binds, but the documentation how to use raw connections is missing.
The issue #107 shows you could get the bind connection engine just using
db.get_engine(app, 'oh_my_bind').execute(...)
.The is missing the documentation about this nice feature.
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