Target domain users accounts existing in SharePoint are getting deleted after running SharePoint Processing Wizard (SPPW).
This has been confirmed and is directly related not to Migration Manager, but to the Microsoft API that is being called.
Here is some information regarding the API:
Please see the "remarks" section in the above link as this is expected behavior if both source and target accounts are present.
Basically, if there is a pre-existing Source and Target user accounts in the SharePoint server then when the SPPW is run it will delete the pre-existing target user account and create a new target account; update the new target account with the privileges and permissions of the pre-existing source account; and then delete the pre-existing source account.