It is indeed the AutoMailUpload that sets the UPLOADSTATE.
The value of the field can be "normal" (0) or "no_link" (1).
The value is set to "no_link" (1) by AutoMailUpload when it isn't able to link a Project or Opportunity to the element. In other words, the badge shows the number of uploaded Mail/Docu/Acti that are not linked to a Proj or Oppo and require addional processing by the user.
Whenever you modify a Document, Mail or Action in Efficy the field is reset to "normal" (0).
There is a second usage of the UPLOADSTATE field, with value "T", when editing an e-mail template, but I don't think that's related to the badges.