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First you should ask this question in the SQL and PL/SQL forum
Nevertheless if you put your 25000 records in a temporary table then you can use the IN operator just fine, the 1000 limit exists only if you manually type all the records.
something like this in your case should work
where TMP_FILTER is a temporary table contanining your 25000 values.
SELETC * FROM [TARGET_TABLE] WHERE [TARGET_COLUMN] IN ( SELECT FILTER_COL FROM TMP_FILTER );