That is not true. I was there. The film that was nearly lost was being made at Pixar. There was never any version of TS2 made by anyone else. I think this idea may come from the fact that Disney owned the Toy Story characters and if Pixar had later gone with another partner studio, it would be Disney making Toy Story movies, not Pixar. This was a major motivator for Pixar to stay with Disney.
I think the other post above is referring to the version of a Toy Story sequel that was in production down in Burbank at Disney in the early 2000's (after TS2 came out). That production was shut down when Disney and Pixar merged in the mid 2000's.