update my_table t1
set my_index_column = t2.rownum
from (
    select id, row_number() over (order by my_index_column asc) - 1 as rownum
    where id = 1
) as t2
where t1.id = t2.id;

import static org.jooq.impl.DSL.*;

public class MyQueryExecutor {

    private final DSLContext jooq; // this gets set via dependency-injection

    public void doTheUpdate(String id) {

        jooq.update(table("my_table").as("t1")).set(
            field("my_index_column"), field("t2.rownum")
        ).from(
            jooq.select(field("id"), (rowNumber().over(orderBy(field("my_index_column").asc())).minus(1)).as("rownum"))
            .from(table("my_table"))
            .where(field("id").eq(id))
        ).as("t2") // <-- this is the line that doesn't work
        .where(field("t1.id").eq(field("t2.id")))
        .execute();
    }
}