As you all know, the Revolutionaries’ base was destroyed by the Blackbeard Pirates, when Burgess revealed its location as an act of vengeance towards Sabo and to try and get their weapons.
As we know from Aokiji’s appearance in Punk Hazard, he’s not afilliated with the Marines or World Government anymore, but he’s on “the other side”. Which might either mean, pirates or Revolutionaries. Pirates wouldn’t make much sense because of Aokiji’s sense of justice, so everyone assumed he’d be associated with the Revolutionaries.
However, later on, in Dressrosa, we find out that Aokiji has connections with the Blackbeard Pirates, and might have given them some info.
So the main theory is that they somehow got away. But what if, Aokiji, knowing about Blackbeard’s plans because he is associated with them, and perhaps being a big unkown player on the Revolutionary side, warned Dragon about Blackbeard’s intent to attack Baltigo?
I’m not saying Blackbeard knows about Aokiji’s association with the Revos, because if so Blackbeard would never let that information leak to Aokiji, but if Aokiji is on the “other side of the grass” where it’s greener, then he may just be helping the Revos and playing double agent on Blackbeard’s crew, and ended up saving the Revolutionaries!
*Theory by Overhaul