From my reading I would say yes, since there's no overlap in what the archetypes replaces, you would just lose all SLAs since you don't have any emotional focus, am I right in my understanding?
As a follow up question, if I were to dip in Dreamthief Rogue could I then gain the SLAs from the spiritualist as I would now have a emotional focus on my char?
Yeah, no, the fractured mind references the emotional focus of the phantom and the phantom blade removes the phantom - that's a pretty clear conflict. Though doing it the way you suggest by dropping the conflicting feature from the fractured mind is a reasonable house rule. As to how that house rule would interact with another house rule to get the emotional focus from another class - ask your GM.