The medicines used to treat HIV are excellent at suppressing HIV-virus replication and preventing destruction of immune cells, but the medicines are unable to eradicate the dormant, or sleeping, copies in immune cells.
In the case of the Mississippi baby, we know she was exposed to HIV, had HIV in her blood, and that at least some cells in her blood were found with sleeping virus though we will likely never know if those cells were from the child or maternal cells that had been transmitted during pregnancy or birth.