I have a similar problem to one that was asked here at the end of last year... I have the need to get FME to truncate all of the writers in a workbench regardless of the number of features being written to them. Setting the properties of each Feature Type works perfectly except if there are NO features being passed to the writer...
I also have users out there with MXDs which reference all 18 of these SDE feature classes, so deleting them before (or as) the workbench starts is not an option - it has to be a truncate.
I have a Python guru looking at it at the moment, but it would be nice if someone on here has had a similar experience and can offer an alternate solution to cutting code.