You can try to format the SD card, but i think it won't work... If it doesn't work try to search for Odin and the files to restore to stock ROM, maybe it can fix the partitions... The SD card partition option in CWM i never used, so i'm not sure what it does in this case.
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Phone: Note 3 N9005/Nexus S i9023/Samsung Galaxy S3 I9300
Recovery: ClockworkMod Recovery
Rom: Stock Touchwiz Android 4.2.2. with Xposed
Kernel: Ultimate Kernel