Hi Jay.  The Master Categories are stored in an XML file at the end-user level.  By default, they're located at:

C:\ SmarterMail \ Domains \ [DOMAIN] \ Users \ [USER] \ userConfig.xml

 

In the code, you'll be searching for:

<ContactCategories>
    <Category>Category_Name</Category>
    <Category>testCategory</Category>
    <Category>MasterCategory</Category>
  </ContactCategories>

So I found out how to fix this issue after searching through my backups. So if anyone else runs into this situation, here's how to fix it. Still doesn't tell me how this happened in the first place, but it only happened to one user and not the rest of the users I have on the mail server.

 

Here's the location of the Master Category list, it's located under each individual user account in the SmarterMail folder. The same user folder that would house their email. The Master Category list is located in userConfig.xml and is located between </Contact> and <Signatures>. It would look like this:

</Contact>

<ContactCategories>

    <Category>(whatever the name is)</Category>

    <Category>(whatever the name is)</Category>

    <Category>(whatever the name is)</Category>

    <Category>(whatever the name is)</Category>

</ContactCategories>

<Signatures>

 

Now in the case of this particular user, the <ContactCategories></ContactCategories> section was totally gone from their userConfig.xml file. So I had to put this section back in thier file and then restart the SmarterMail service. Now their Master Categories are back again. Now with that said, their AddressBook.xml file also had the <Category></Category> missing from each individual contact that they previously had assigned. So I had to restore a previous backup of AddressBook.xml from a few days ago to get their contacts back to whatever Category that was originally assigned to them. If you wanted to, you could put the categories back manually, but it would be much faster and easier to replace the file from a backup and the you have to restart the SmarterMail service again.

 

Hopefully this helps someone out if they run into this situation.