Хм. Попробуй включить отладку алхимии, она будет все запросы в лог писать
2019-03-11 14:32:05,967 INFO sqlalchemy.engine.base.Engine SELECT CAST('test plain returns' AS VARCHAR(60)) AS anon_1
2019-03-11 14:32:05,967 INFO sqlalchemy.engine.base.Engine ()
2019-03-11 14:32:05,968 INFO sqlalchemy.engine.base.Engine SELECT CAST('test unicode returns' AS VARCHAR(60)) AS anon_1
2019-03-11 14:32:05,968 INFO sqlalchemy.engine.base.Engine ()
2019-03-11 14:32:05,979 INFO sqlalchemy.engine.base.Engine SELECT CAST('test plain returns' AS VARCHAR(60)) AS anon_1
2019-03-11 14:32:05,979 INFO sqlalchemy.engine.base.Engine ()
2019-03-11 14:32:05,979 INFO sqlalchemy.engine.base.Engine SELECT CAST('test unicode returns' AS VARCHAR(60)) AS anon_1
2019-03-11 14:32:05,979 INFO sqlalchemy.engine.base.Engine ()
2019-03-11 14:32:05,980 INFO sqlalchemy.engine.base.Engine PRAGMA table_info("client_groups")
2019-03-11 14:32:05,980 INFO sqlalchemy.engine.base.Engine ()
2019-03-11 14:32:05,981 INFO sqlalchemy.engine.base.Engine PRAGMA table_info("customfields")
2019-03-11 14:32:05,981 INFO sqlalchemy.engine.base.Engine ()
Судя по логам, вроде как даже и создает. Но в sqlitebrowser не видно все равно нихера.