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They would still be able to use Susano'o possibly. However their chakra reserves wouldn't be restored due to their portion of chakra being sealed within Shiki Fūjin.
That is what my reply was to Q Of The Sharingan. I believe we have the same thought process on this situation.
Also take into account orochimaru's curse marks, which i could debate as a fuinjutsu. Kabuto was able to extract the chakra used to create it out of the seal on anko's neck and add it to his own, but i have a hard time believing that orochimaru lost the chakra he created the marks with permanently, as he would need monstrous reserves seeing as how he gave 10 children curse marks, along with kimimaro, sakon, ukon, tayuya, kidomaru, jirobi, and sasuke.