MY current project somehow lost all audio files, I ran CWAF and found these files to be marked as "Orphaned". How do I re-associate these audio files with the project? "Find Missing Audio Files" never opened up for me to search and tell the project where to look. Running Sonar Producer 8.5.3 and Windows 7

Copy paste them from where they are to the projects audio folder. Simple. 

They are already in Project-Audio. I can click on each one individually and they play in WMP, however when I ran CWAF they all show up as orphaned. When I open the project it opens without any audio files, also surprised "Find Missing Audio File"  dialog box never opens.

It sounds like something in the project file corrupted.
Cactus' suggestion is probably best, especially if it's only happening in one project.
 
A less-likely cause could be incompatibility between Sonar8.5 and your OS (i could be wrong but suspect it was only supported until XP).

 I have 8.5 on W 10. I don't use it but it certainly opens. I just install it to get V Vocal and the Lexicon reverb. 
 
It's weird if the audio is actually in the projects audio folder and it still does not load. 
Did you change the name of the project? 
Do those audio files have the exact same name? 
 
Example Projects name " Shook up"  Audio files should read " Shook up, Bass 1 ,rec(324) .wav "   
 
If you changed the name of the song to "Shook up 2" you will loose the connection to the audio. 
Options are to rename the audio files so they match the song title or try drag and drop from the media browser. 

Is a strange issue. Didn't change the name, and yes the wav files have the exact same name. Still CWAF calls the files "orphaned". Not sure what you mean by drag and drop from the media browser tho.

have you tried saving the project with a new name to a new folder
use the "Save as" function.

Yes, tried that Chuck. Same result :(

You can drag and drop audio files directly onto the track view. 
I'm assuming the project opens with a bunch of blank tracks. 
If not insert new audio tracks and drag and drop the wave files there. 
Only thing is if a track contained start and stop edits and punch ins that track will be broken up into multiple wave files. There fore the numbering system that only Sonar can decipher. 
In that case you just have to listen to them and decide where they should be on the time line. 
This method won't be much fun on a complicated song with 30 wave files in the audio folder but it might be your last resort other than just redoing all the tracks. 
 
It shouldn't matter, but you haven't changed the sample rate? 

Cactus Music
Did you change the name of the project? 
Do those audio files have the exact same name? 
 
Example Projects name " Shook up"  Audio files should read " Shook up, Bass 1 ,rec(324) .wav "   
 
If you changed the name of the song to "Shook up 2" you will loose the connection to the audio. 
Options are to rename the audio files so they match the song title or try drag and drop from the media browser. 

 
Totally untrue. Renaming a project does not lose its file associations. Sure it assigns names to newly imported audio files based on the project name, but it retains the file association thereafter. If it worked the way you are implying that would be ridiculous.