The code is exactly what I previously posted
$av_url = $mosConfig_live_site . '/images/comprofiler/' . $filename;
Then I run an SQL query that updates the avatar in smf's member table.
Ok I've looked in the smf_member table and the links are stored correctly. So your line of code above is doing it job.

However when the following line of code is called in mod_smf_login.php:
$context['user']['avatar']['image']
the SMF Avatar URL is somehow added to the front of the correct avatar link stored in the database thus making it incorrect.

When you say you are changing the link, is this in the database or on the members SMF profile? Be explicit, something is going wrong here.
The link I'm changing in an effort to get the correct Avatar Path is the SMF Avatar URL which is being added to the front of the link. Only SMF Forum Admins can change this link by going to:
admin > Attachments and Avatars > Avatars Settings
Then under
Server-stored avatars section I changed the
Avatars URL: field to nothing. Becasue this is the URL that keeps being added to the front of correct avatar link already stored in the smf_member table. Unfortunetly even with the SMF Avatar URL set to nothing a single backslash is added to the URL thus making it invalid:
/https://www.cbavatarurl.com/images/comprofile/theimage.jpg
So my question is
Where is the following array constructed?$context['user']['avatar']['image']
Wherever this is constructed is where the URL is being added to the front.
Or maybe there is a setting in either SMF or CB or JSMF that is not set right which is making this all come out weird.
I hope this was specific enough. Thanks
-barnett