Yes, they are still counterfeit, and will not morph into genuine notes any time soon. They were not condemned because somebody "thought" they looked counterfeit, but on the basis of incontrovertible documentary evidence.
Many of the 1852 English Issue surviving notes are counterfeits as well, sadly, but there are some genuine examples. The Bank had a very bad experience with that issue, and placed no more orders with the printer.
Valuable information on the English Issue was published in the CPMS Newsletter issue of Dec. 2004.