Ah gee whiz... we know what is causing it.
It was the look ahead latency compensation, other wise known a Plugin Delay Compensation or PDC getting baked into the project when the Perfect Space was used.
When the instance of Perfect Space was removed the Plugin Delay compensation didn't fully release and now you have a weird timing and trigger glitch going on.
The very best thing you can do is send that corrupt project to Noel and let him dig in to the internals so he can see what's up.
This issue has been going on for 10 years plus. It's just part of the SONAR experience.
I use the work around I recommended above because you have to avoid the problem rather than hope to fix it.
I figure that the PDC operation is some of the most complicated aspect of SONAR, and I appreciate it when it works because frankly a DAW without functional PDC is no fun to use... it would suck to not have PDC... so this one little issue is something I'm willing to work around.
As I say, I sure wish Cakewalk would spend more resources on this type of stuff than making new add-on gadgets to give away for 1/2 price.
The PDC stuff is important.
Oh BTW, the easiest way to turn the audio engine on and off is too simply restart SONAR. If that doesn't make the problem go away... then you know you got a problem. Simples.
all the best,
mike