The optimization process and recommendations:

1. Avoid Calling Functions With Indexed Columns (query line: 20): When a function is used directly on an indexed column, the database's optimizer won’t be able to use the index. For example, if the column `id` is indexed, the index won’t be used as it’s wrapped with the function `LOWER`. If you can’t find an alternative condition that won’t use a function call, a possible solution is to store the required value in a new indexed column.
2. Create Optimal Indexes (modified query below): The recommended indexes are an integral part of this optimization effort and should be created before testing the execution duration of the optimized query.

Optimal indexes for this query:

CREATE INDEX example_table2_idx_id ON dbo.Example_Table2 (id);

The optimized query:

SELECT
        LOWER(CONVERT(VARCHAR(32),
        CONVERT(VARBINARY(32),
        r.id),
        2)) AS id,
        r.id AS respondentid,
        'new' AS qtype,
        r.email,
        r.language,
        'Y' AS is_online,
        r.createdDate AS time,
        r.createdDate AS date_sent,
        r.state AS state,
        r.sourceID AS sourceid,
        req.id 
    FROM
        [Example_Server1].[Example_Database1].[dbo].Example_Table1 AS r 
    LEFT JOIN
        [Example_Server2].[Example_Database2].[dbo].Example_Table2 req 
            ON LOWER(CONVERT(VARCHAR(32),
        CONVERT(VARBINARY(32),
        r.id),
        2)) = req.id 
    WHERE
        req.id IS NULL