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It turned out that the behavior was caused by SQL_MAX_ROW which at some point after superset 0.15.4 got split into SQL_MAX_ROW and DISPLAY_SQL_MAX_ROW.
In my custom config I had the former set to 1000 and didn't notice that in more recent versions this is now set in the latter...
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Superset version
0.18.5
Expected results
CSVs downloaded in SQLLab contain all rows defined by the query.
Actual results
Regardless of the row limit set in the SQL statement, the CSVs only contain 1000 rows of data.
Steps to reproduce
Download the CSV from a query that returns more than 1000 rows and count the number of rows in the resulting CSV.
Investigation
It seems that QUERY_SEARCH_LIMIT and DISPLAY_SQL_MAX_ROW don't influence this behavior.
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