I reckon she's back in the present day but something will happen so she goes back to the eighties as there's going to be a third series... perhaps running about in the hospital with the Gene Genie after her will make her collapse back into a coma or something?!
The way I saw it was she is now in a coma in '82 which has enabled her to wake up in the present. But there is obviously unfinished business back in the '80's so she will need to go back to help Gene Hunt, probably by slipping into a coma now to allow her to wake up again back then.