@healthcareaa there's no need to update your preferences versioning unless there are specific keys that have been added or changed in that schema you need to take advantage of. Existing deployed configurations for previous versions of Connect continue to work as the apps update. If you do want to make changes to those managed settings, know that Connect reads in those settings on launch - which typically occurs as part of the install process. In that case, I would push the new configurations before applying the updates.

One trick. If the new keys don't conflict with your existing keys you can create a whole new profile with the new keys and just push that as a companion to the existing profile. 

However, and this bit me, A lot of the preference keys are part of a larger dictionary. For example, Jamf recently added the PasswordSyncBlockList key to not prompt specific users to log in to Jamf Connect. However, it is part of the PasswordPolicies dictionary and I already had other keys in that same dictionary in my original config profile. You can not have the same top level preference key in two different profiles. macOS will only recognize one of the settings for that key.