Because I pulled the data into a temporary table from the main db, this script wasn't working. I figured out that because I took the data as is, the field was of type CHAR(20)...and it's not something mentioned in my original post so you wouldn't have known. When I changed your script to...
SELECT invoice_id
FROM <YOURTABLE>
WHERE LEFT(RTRIM(invoice_id), 6) NOT IN
(
SELECT DISTINCT LEFT(RTRIM(invoice_id), 6)
FROM <YOURTABLE>
WHERE (RIGHT(RTRIM(invoice_id), 4) = '0001')
)
...it worked beautifully.
Thanks for putting me on track with this.