I just left a comment in the Field Collection issue queue and thought it’d be good to spread it more widely; maybe people need this fix.
For anyone still getting burned by this bug (or for that matter getting burned by using Node Clone on nodes with field collections), first apply my previous patch (or bderubinat’s, but I haven’t tested that one). That will stop further damage.
To repair your previous entries and ensure that, for example, removing a field collection entry doesn’t remove it from other nodes from which you didn’t want it removed, you can implement this script I’ve detailed in a gist: https://gist.github.com/wizonesolutions/5567549
It will give new
item_ids to field collection items that it detects as appearing more than once. All my testing has indicated this is safe, but if not, please leave a comment on the gist. I hope this helps someone.
Thanks to Project Ricochet for sponsoring my time on this.