Build 4.0.0.77 of xlsgen exposes table auto-filters in the object model. So beginning with this build, it's possible to either create or edit existing auto-filters in tables, and write them back in XLSX and XLSB files, thanks to the AutoFilter member exposed in the table results interface.

So here is how it works :

IXlsWorksheet worksheet = workbook.WorksheetByIndex[1];

// get the first table
IXlsTable t = worksheet.Tables.Item[1];

// edit the filter in the second column of the table
t.DataResults.AutoFilter.CustomFilter[2].CustomExpression = "> 2";

// remove the filter in the third column of the table
t.DataResults.AutoFilter.CustomFilter[3].Delete();