I think Souhaku is still in there, but either Nagi himself, or Nagi with Aya's help, is preventing him from taking over the same way Makiko's eyepatch prevented her dragon from taking over her.
Nagi's new eyepatch is working on several different levels.
1) It's an allusion to Shin and the parallels that are evident between Shin and Nagi.
2) It's an allusion to Makiko and what I've stated above.
3) Oh! Great has been using the theme of the Eye for quite a while thoughout the manga, so this is yet another incarnation of it.
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