I have an old project that is just being a total pain, crashing crashing crashing. So I've been opening it in safe mode and turning on single instruments at a time and trying to do exports so I can archive all the crap and get to mixing. 
 
Well, I got most of the way through, saying "no to all" when I've turned on the plugin of choice (feature request: being able to go forwards/backwards through these prompts!). I got things working okay and saved the project a few times.
 
Now when I load the project all the subsequent plugins, instruments AND effects, are GONE. Not even bypassed, like totally removed from the project. Is that behavior as intended? If so I've got some problems with that. 
 
Anyhow, I think I've got a backup I can pull from so I'm not losing my mind just yet, but sheesh what a major hassle.
 

Any commenters on this? Lately I notice it takes me a ping to grab everyone's attention. Maybe I need better copywriting skills!
 

If you open a project in safe mode, disable one or more plugins and then save the project, they will effectively be delete from the project.
To mu knowledge, Safe Mode has always worked in this way and the only real workaround is if instead of simply saving, you'd need to do a "Save As" with a different name.
I'm afraid your plugins will be permanently missing if you've over written the original file
 

Which version of Sonar were you using when you created the project? If I were you I would keep it installed on your system for situations like this. I'm not letting go of Sonar 7 because I have had similar problems to yours with some old projects.
 
By any chance are you using the 64-bit version of Sonar to open a project created in an earlier version at 32-bit?

Any time I attempt something like that, step #1 is always to make a copy of the entire project and then work from the copy. 'Cause you know, you just never know.
 
What happens when you bring up the project? Does it literally crash, or just complain about missing plugins? IOW, is the project corrupt or just referencing a bunch of since-retired plugins?

When loaded with all plugs, the project will run, about 50% of the time stopping playback produces a "good" crash (ie, the one where it prompts you to send Cake info and closes...when it does this I can re-open right away...). When bouncing down a clip it produces a "hard" crash (ie I have to kill it in task manager and it locks up the audio interface drivers and I have to reboot). Oddly, exporting a clip does not have any crashing effect.
 
Anyhow, I've got a backup of the project (whew, just did a massive backup last month!) so I'm going to try bringing it up and saving some effect presets this way I can strip it down and build it back up. I swear though I've spent about the past 1.5 years dealing with things like this over this album. I think the next one is going to be all Cake-included plugs. Don't get me wrong, it's my fault for rebuilding my DAW in the middle of an album project. I should've rendered stems for everything beforehand!
 

Another non-plugin oddity about this project (this is a good example of totally random weirdness that occurs): when I first open the project and click on a track every track expands a little bit. I have to manually shrink the track down all the way, which all tracks follow suit. Note, I'm not holding down CTRL here, just adjusting one track height, but all the tracks follow even thought they're not selected, quick grouped, or grouped. THEN, I open the track up to the correct height and everything behaves again. Even if I save the project it does this every time.
 
And it's separate for bus tracks. And regardless of how I save it (always with the Browser in the Dock, and the Dock on my 2nd montior), it always opens the same way: nothing in the dock and the dock at the bottom of the main screen. Eesh.
 

Sounds like you've got Auto Zoom enabled.
 
Now I've wrapped my head around it, I use it all the time

Oh I use it all the time too, but the initial behavior on load is not standard. Plus, it does this every time. 
 
The project is all sortsa hosed. I think I'm going to try bouncing down all the audio tracks and rebuilding them a discreet new project and see what happens. It sets me back oh, like forever, but it will keep me moving forward. Now playback works but on Stop the project crashes. Grrr!