This is becoming the one thing that is sticking up my butt about Sonar. Automation is turning out to be quite cumbersome and unreliable in Sonar. I always took it for granted it would work as needed when I actually start digging into it and have hit nothing but problems and brickwalls (including envelopes not working reliably which is of course a major problem in large projects).
I think the Baker's, now that they have sorted out so many of the simple but crucial things users have been requesting, should really take a fresh look at how automation works. That is from a reliability/stability aspect and from a workflow aspect.
That is not helpful in this regard of course so to not just drop a dump and walk away I think what might help is that once you create an envelope you like on a specific track you should Freeze it (and make sure the freeze worked/wrote the desired automation) then move on to whatever else you need to do. If you need to adjust it later on you can always unfreeze it, do what you gotta, then refreeze.
Remember you can freeze a track and freeze a synth or both at the same time. Two different things so if this is a synth thing the maybe freezing the synth is all that is needed to hang on to your automation and you can still deal with the track effects and whatnot on top of that.
I guess now you could also record any of this into an instrument/Aux track and use that as you work on the project (and mute the original synth/FX/etc).
There are certainly lots of workarounds now but definitely this hinkey automation stuff needs some forensic exploration.
Cheers.