Any way to recover settings?

Restoring a backup is the only way I know to get files back that have been altered or removed by accident.
 
Screensets are stored per-project so changing SONAR configuration should not affect them.
 
I did not think a partial personalization (SHIFT while opening SONAR) overwrote data, it should only replacing missing files in the user directory. A full personaliztion overwrites files in the user directory and restores some registry settings. It is launched by hold the CTRL key while starting SONAR or renaming the SONAR Platinum folder in %appdata%\cakewalk as described here

MakerDP
OK so if I held SHIFT while opening the project in safe mode to choose which plugins to disable, would that cause the screensets for that project to disappear?

No not at all. I have opened in safe mode many times and never lost Screensets.
Screensets are stored and saved within your project. If you lost screensets, I suspect a Lens possibly being the culprit. Are you using Lenses ?
 
You can also load a project with stored screensets and import them to another project.

OK now I have a bigger issue... I cannot open any projects that use the Two Note Wall of Sound III plugin.
 
This is the source of all my woes apparently and is frustrating to say the least! I'm not sure I will be open any old projects without safe mode at all since I use it pretty much for all my guitar tracking.
 

The minimum requirements for that plug in require an Audio interface. what are you using ?
http://www.two-notes.com/en/wall-of-sound

Tascam US-16x08 but I don't think that's the issue.
 
Once I load the project in safe mode and say "no" to WOS III I can add the WOS III plugin back in no problem (losing my settings unless I saved as a preset in WOS of course... grrr), work with WOS no problem, save project no problem then once I try to re-open... no dice. Have to load in safe mode and disable it on all tracks again.
 

Could try the production release. If that fails, try rolling back to the version  you were running before the Early release. Assuming the problem started after installing the Early Release. If the problem happened before installing the Early Release, the cause is likely something other than SONAR.

If the current version does not fix the problem and rolling back to to the version you were running before does solve the problem, create a Cakewalk problem report. Make sure to include the plug-in details (such as 32/64bit, version number) and last version of SONAR that worked correctly.
 
To roll back SONAR,
run the Command Center
right click on the SONAR item
Select the appropriate version from the Rollback option on the menu.