Clarke himself said that the print sequels to 2001 each take place in alternate parallel universes. Therefore in each of the sequels the powers and motives behind what the monliths do can be completely different - each is effectively a re-imagining of the basic premise. Changes between universes include how Floyd, who had also been "uploaded" in 2063 is absent from 3001, and how the epilogue of 2010 is set in 20,001, with monoliths present on Europa, when by the end 3001 monliths have left the solar system, and how 3001 acknowledges that the Soviet Union dissolved in 1991, despite it's important roles in 2001 and 2010, and pushed back the chronology of the first two novels to 2030 and 2040, respectively (Yes, in the 3001 timeline the Discovery mission doesn't actually take place in 2001.).

The original conception of 2001 both film and novel is as I outlined. Bowman was not merely being "uploaded" into a computer in that film.

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"You miss 100% of the shots you don't take" - Wayne Gretzky