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I don't think that's allowed (I don't see what you mean by "compare arrays directly works"), arrays/lists are for the IN operand not = , the order would likely break it and empty arrays are not allowed either.
You should be able to redefine your query so it returns a number of a boolean, for instance if you want to check that code array return empty:
CustomSql "select size(array_agg(code)) from table where IN ( 'CANCELLED', 'REPROGRAMATED', 'GRACE' );" = 0
or just:
CustomSql "select count(code) from table where IN ( 'CANCELLED', 'REPROGRAMATED', 'GRACE' );" = 0
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