If the User Directory Group has the "Automatically link Managed Directory Accounts" option enabled, then when the Directory Sync runs, the linking information will be taken from AD. Any manual linking changes would be reverted. If linking is being set manually, then the "Automatically link Managed Directory Accounts" option should be deselected.
More information from:
"At the bottom of the Directory Group dialog, select the Automatically link Managed Directory Accounts check box to have existing managed directory accounts set as linked accounts on the imported user. For details on linked accounts, see Linked Accounts tab (user).
Based on the setting of the directory asset's Managed Objects attribute, the attribute values are used to match up with existing managed directory accounts in Safeguard. The Safeguard user’s set of linked accounts will periodically synchronize with the directory and be overwritten with the values from the directory. Any changes to the linked accounts made manually to the user are lost at the next directory synchronization (see Sync additions every under Management tab (add asset))."