ok two things, you can only filter against fields that are known by gen_setup (so, id is not working, take name for example), and you have to include in every case the owner-id field in the gen_setup, even if you don't want to change that:
<?xml version="1.0" encoding="UTF-8"?>
<packet version="1.6.3.0">
<webspace>
<set>
<filter>
<name>testing.ch</name>
</filter>
<values>
<gen_setup>
<name>testing.com</name>
<owner-id>1</owner-id>
</gen_setup>
</values>
</set>
</webspace>
</packet>