That's default behaviour and I don't think it can be changed. Best thing to do is write to a temporary location and then use a SystemCaller to call a zip command line. I know 7Zip is capable of adding to existing zip files.

Here's one I used a while ago to bulk-add a lot of files to a lot of existing zipfiles.

As an alternative, you can use the ZipArchiver transformer from the hub.

This is what I use, and prefer over the SystemCaller.

Hmm, that's funny, because a zip file has been treated as a folder previously in FME (I think)! Thank you for the reply!