Lopes died in a 2002 car crash in Honduras. She was 30.
Her family and fans criticized the vocal group for replacing Lopes with Japanese pop star Namie Amuro in a 20th anniversary edition of the hit song.
But the surviving members of TLC -- Tionne "T-Boz" Watkins and Rozonda "Chilli" Thomas -- told TMZ they don't own the master recording rights to Lopes' rap and couldn't legally use it in the new version of the song.
"We were forced to use a creative way to honor Lisa's memory and celebrate this milestone with the fans," Thomas told the celebrity news website.
"We have and always will protect our sister's legacy as TLC consists of the three of us collectively. ... There will never be a replacement for Lisa or any members in TLC."