All Vendor Codes have a number of Attributes, including one called "Inactivate Classifications".  If that particular attribute contains the name of a Classification Code, then any pre-existing Classifications with that code will be inactivated for the uploaded accounts. This applies to pre-existing classifications on both account- and name-level.

The following page is in TA's online help:
Setting Attributes for an Account Data Upload Vendor File Code

Inactivate Classifications

Indicates a pre-existing classification that should be inactivated for the uploaded accounts. This applies to pre-existing classifications on both account- and name-level.

If this option is undesirable, the value should be removed from the Attribute field for that Vendor Code.

The backend method to check for this attribute is in this query:
 
SELECT * FROM UPLOAD_FILE_CODE_ATTRIBUTES
WHERE UPLOAD_FILE_CODE = {Vendor code}
AND ATTRIBUTE = 'INACTIVATE_CLASSIFICATIONS';

The resulting Attribute Value will be the Classification Code used to determine the records that will be inactivated.