To restate your question: You have an Excel document with cells that contains new lines. You want to export this document to CSV and the new lines within the cells are corrupting the CSV file.
Removing Newlines
It appears that you have tried removing the new lines from each cell as they are written to CSV, but state that it does not appear to work. In the code that you give you replace just the \r characters, but not the \n characters. I would try this:
String col = columnName.replaceAll("[\r\n]", "");
reportColumn.put( "column", col );
which will replace all both types of characters that could be interpreted as newlines (indeed on Windows, a newline is usually two characters together \r\n).
As far as your regular expressions for removing newlines go here is the rundown:
",," // Removes two commas, not newlines
"." // Removes all characters, except newlines
"\r" // Removes the "carriage return" characters (half of the Windows newline)
"\n" // Removes the "new line" characters (half of the Windows newline)
"\r\n" // Removes a Windows newline but not individual newline characters
"\\r\\n" // Same as "\r\n" but the escapes are handled by the regex library rather than the java compiler.
"[\r\n]" // Should remove any newline character.
"[\\r\\n]" // Same as above but with extra escaping.
Writing Escaped Newlines
It should be possible to generate CSV files that include newlines within the cells. Indeed Excel itself can do this. There is an ExcelCSVPrinter java library here that will do all the escaping you need for you: http://ostermiller.org/utils/CSV.html
This is a single line of excel format csv:
"cell one","first line of cell two
second line of cell two","cell three"
http://ostermiller.org/utils/CSV.html also provides an ExcelCSVParser Java library for reading Excel CSV format like that.