After Anne Boleyn's execution, her remains were hastily buried in the chapel of St. Peter ad Vincula with no stone to mark the spot where they rested. After she was dead, Henry set about the task of erasing his wife from history. He was rather proficient at it.
It appears most of Anne's portraits were destroyed. The only contemporary portraits that survive are a badly-damaged lead portrait medal, the sketch made for her coronation feast, and - possibly - a Holbein sketch. The other images we have of her were painted in her daughter's lifetime.
Anne's renown and the amount of curiosity this lady inspired meant there once had to be many portraits of her. (Consider the number of portraits created during the short reign of Kateryn Parr.) It is almost a certainty that Anne sat for several portraits. We have no record of a Holbein painting, but it's highly possible one was done, considering Henry's preference for this artist. There may have also been miniatures.
Once a painting of a monarch was created, artists were frequently commissioned to make copies for families to display in their own homes. In those days, prominently displaying a portrait of the monarch was a popular way of demonstrating allegiance, and portraits were also frequently given as gifts from monarchs to favored courtiers and diplomats.
The famous "B" pattern portrait likely is based from a image of a younger Anne, painted before she was queen, during the time when Henry was perusing her as a love interest. After she was queen, Anne would have worn finer jewels that she's pictured in that image; in her portrait medal, she may be wearing the "consort's necklace" (she also wears it in the Nidd Hall painting.) Charles I had a painting of Anne Boleyn copied in miniature by John Hopkins the Elder. It was noted in a 1625 inventory of the king's art as "don by Hoskins after an oweld pictur." It may have been the original image on which the "B" pattern portraits (The NPG/and Hever versions) are based.
So, what happened to Anne's portraits? After her fall, most people probably destroyed them. Courtiers would not have wanted to have the image of a traitor displayed in their home for fear of angering the king. But a few may have survived the purge. Some may remain hidden away to this day.
One full-length portrait of Anne Boleyn supposedly survived in the collection of Baron Lumley, an art lover who collected portraits, especially those of Holbein. It appears after Anne's fall, Lord Lumley chose to put the portrait in storage instead of destroying it. If Anne's portrait was painted by Holbein, that may be the reason Lumley decided to preserve it.
In the 1590s, Lord Lumley had a dispute with Queen Elizabeth over a debt, and all of his property was inventoried. The painting was one of the items that was noted in the inventory. (Of the over 200 portraits in Lumley's collection, only 30 can be identified as extant today.)
The Lumley portrait was known to have survived until the latter part of the 1700s, but after that, it vanished without a trace. It was presumably sold off from the collection, as the other pieces were, but who bought it, and what did they do with it?
It's also possible that portraits still exist but are not identified or are mislabeled. Our "image" of Anne may not match the reality of her appearance, and so we may already have portraits of her we simply do not recognize.
A sketch by Holbein of a woman labelled as Anne Boleyn still exists and is definitively identified in the Royal Collection as being Anne, but people insist it cannot be her because the light reddish hair and double chin which do not match how we picture Anne.
Perhaps the Holbein portrait is still out there somewhere, waiting to be rediscovered. One can hope.