By syncing NAND, it means the Wii and Cache folder. As long as those were just generated by Dolphin, then there isn't a problem.
The DC netplay branch didn't sync these so much as it just disabled the Wii folder for the duration of the netplay session, which prevents certain Wii games from working.
The DC netplay branch didn't sync these so much as it just disabled the Wii folder for the duration of the netplay session, which prevents certain Wii games from working.