I think it may be from Rumple’s past. Something he treasured but lost whilst growing up.
Or because Felix said YEARS rather than CENTURIES perhaps the doll has nothing to do with Bae or Rumple’s childhood but is a reminder of something bad that Rumple did whilst the dark one on his quest to find Bae.
In Welcome to Storybrooke, Snow asked Rumple how he lived with himself knowing all the bad things he’s done, and his reply was “you tell yourself you did the right thing and if you say it often enough, one day you might actually believe it”.
We might actually see one of the bad things Rumple did. The doll turning up is to remind him of that.