My first post was poorly worded, but that does clear a few things up. The biggest point of confusion was how he went about getting them back in his ranks after they were beaten, and if it was so easy, why he felt the need to seek out Sora/Riku in Dream Drop Distance.
If that's the case, then there must've been a line in DDD that I misconstrued as meaning something else entirely. I just remember something near the end of the game that implied the members coming from an earlier timeline.
Well mainly how he got them back up was simple due to the numbers:
Master Xehanort himself came back as a result of Ansem and Xemnas being defeated in KH1 and KH2 respectively this would make Xehanort the first of the thirteen darknesses
Xigbar, Saix, Luxord, Marluxia, and Larxene are all in the present and were basically turned back Human then back into Nobodies so that makes the number go up to six darknesses.
The ones from the pasts points would have been Young Xehanort, Ansem, Xemnas, Riku Replica, and Vanitus, this rounds the number up eleven. Thus where 12 and 13 come into play.
We kinda can count both Vexen and Demyx into the count as contingency candidates.
This leads to the last which are Terra and Xion which would make the total up to thirteen. Terra was an obvious choice as his body was fully restored but Terras heart never returned to his body so it was an empty vessel and Xion is basically a replica body so they were able to piece here back.
It should be noted that there are also 20 Replicas that were made during the games events. 12 of them are boss fights in game prior to the final battle with Xehanort. Six were used for the time travelers and Xion. They gave 1 to help with Roxas coming back and there seems to be one missing from that count though I think it can be assumed that Xion technically has two bodies and the first was destroyed when she was defeated.
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"He may be Mr. Clean, but his soul will always be dirty!"