Removing the configuration for a custom alembic_version schema

version_table_schema=target_schema

when configuring the context fixed the same issue on my end and removed the op.drop_table('alembic_version') from the upgrade() function.

If you want to have alembic_version stored in a custom schema, I'd recommend checking the recommended multi-tenancy guide for alembic as an option. This worked well in my case, though, my case is anyway that I want to implement multi-tenancy via separate schemas with alembic.