After hours of debugging, I found what the issue was. Each of my entity class was decorated with the below decorator

@Entity({ name: "table_name", synchronize: false })

I mark all the entities with synchronize: false to avoid any accidental schema changes, as if I enable the synchronization on data source level, it will apply to all the entities (or tables).

Setting this to synchronize: true enabled typeorm to consider this entity for migration, and thus, I were able to generate migrations for all modified entities by temporarily enabling this synchronization attribute for entities requiring migration script to be generated automatically.