If I select a clip in Sonar X1 and delete it also the automation envelope get deleted. In Sonar 8.5 there was an option in the toolbar that said "don't select automation with clips" or something similar (can't recall right now).

Where is this feature in X1? 

Even if I select "clips" in the track header the automation is effected by editing.

Try Edit > Delete and de-select automation.

Edit and delete? Sorry, can't seem to find that...?

From the menu bar, under "Edit"

yeah, there are a bunch of check boxes there in that window.... read them all and select the ones you want .... be sure to deselect the ones you don't want applied. 

there is a default and it is usually the most common option but if you need something else you must choose the options.

In the TV Menu deselect Options->Select Track envelopes with clips

Awesome, thanks!

Finally found it...

Thanks Giannis for the question and FBB for the answer...(once again!) conga

As I am reading this, I am wondering if it is possible to place any automations onto a separate track to the clip. I might have a look into this tonight, when I get home from work. I just fancy being able to keep my synth automations separate from the MIDI track...

All automation should appear in the Audio track, that's assuming you're running split Audio/Midi tracks for your synths, and not simple instrument tracks, and also assuming there's no Midi Fx you're automating.