It does cause some confusion when "Prime Earth" is both the name of the continuity and the name of a reality in that continuity. For example, the Darkseid of Earth 22 (ie Kingdom Come) is dead but that is still a Darkseid of the Prime Earth continuity.
I think we are talking about two different soft reboot. I'm talking about the one that happened in Action Comics #976 which seems to have dumped large parts of the Reboot continuity up to then down the tube. For example, the Crime Syndicate's death in the Forever Evil storyline don't seem to have happened in the post Action Comics #976 reality as Superman in Superman (Volume 5) #9 talks as if they are still alive.
Thanks to DC's inability to keep its hands off the freaking soft reboot button we can't trust anything said or displayed before the reboot until it is reiterated in the post soft reboot comics.
Heck, we could be looking at the Crime Syndicate from the Anti-matter Earth who we last saw being locked between realities as happened to their Earth-Three counterparts only to escape in time to die with their death in Crisis.
Except when Superman describes the Crime Syndicate he uses the present or future present tense. If they were gone he should be exclusively using the past tense.
More over in the Post-Flashpoint Prime Earth history they came over once not "often" as those not killed at the end of the Forever Evil storyline got a serious case of dead by the end of the the Darkside War saga. So if that aspect of their interaction with Prime Earth changed so why not their deaths?
As mentioned in the EARTH 2 & CRIME SYNDICATE QUESTION (SUPERMAN #9 SPOILERS) thread over at CBR hypertime plays total havoc with continuity - history is misremembered or even altered as various timelines of an Earth interact with each other. It is to put it bluntly a mess. Never mind there it has been demonstrated there are 53 universes in the local multiverse.