There is no way in hell that Michael is singing the Beat It vocal live in This Is It, but I think the vocals are coming from a composite of sources - I think this includes any previous tour, whatever they may have recorded at the TII rehearsals, and possible studio sources. From what I can tell of the movie, they used a composite of sources in an effort to make sure the audio track was always synchronized with the video. This goes for most of the songs in the movie.
Some songs are definitely live in the film, I would say these are mostly or entirely live:
Wanna Be Startin' Somethin'/Speechless
(I have a feeling that the style of this particular rendition plus the unique and quality performance Michael puts on pushed the film editors to retain most, if not all of the TII rehearsal vocal)
Human Nature
(The best vocal performance in the entire film, but comparisons with the original Human Nature preview, http://www.youtube.com/watch?v=FsVYuGwAuR0 indicate that the track may have been pitch corrected or otherwise altered)
Jackson 5 Medley
(Michael never really had trouble singing this one, even in the rougher HIStory years - I suppose it is possible that they took this from another live performance, but I doubt it)
I Just Can't Stop Loving You
(The roughness and unique quality of Michael's vocal track here appears to be from the TII rehearsals)
Black or White
(He never would have sang with this kind of falsetto in an actual live performance, so I think this is also from TII)
The following songs have some live portions, but are clearly mixed with previous live or studio vocals:
Smooth Criminal
(listen to the ends of certain verses and most of the chorus vocals)
Man in the Mirror
(the "HOO" section is definitely live)
The Way You Make Me Feel
(the introduction and very end, where the band accidentally stops early, are live - though I have my suspicions that parts of the introduction are taken from other sources)
Beat It
(The "HOOO" intro and some of the shorter "Beat its" in the first chorus, as well as some of the ad lib section, appear to be live vocals, but the rest is almost certainly lifted from another live performance)
These songs are almost entirely prerecorded from a studio or live performance, and you can actually hear how the film editors cut audio in order to fit with the video:
Jam
(The vocals here are at times not quite on the beat with the rest of the band, but it's clearly from the original Dangerous album track)
They Don't Care About Us
(hear the pacing of some of the lines, it's clearly the studio track Michael recorded back in '96 but it has been edited to fit with the video - compare this with the first clip released to news outlets when Michael passed back in June 2009)
Thriller
(is clearly just playback from the album version, nothing special - though the fact that the vocal has not been edited much leads me to believe that this was actually going to be playback in the actual concerts)
Earth Song
(has clearly been lifted from the "What About Us" demo leaked on the Dangerous DAT tape as seen here http://www.youtube.com/watch?v=Fu3M_85aTV0)
Billie Jean
(has been taken from this demo of Billie Jean http://www.youtube.com/watch?v=MGlqlkkryFE or at least a similar demo, which is curious since we have knowledge a live TII rehearsal vocal exists - see this commercial http://www.youtube.com/watch?v=Jnpx42yv7h8)
Now this are just my own suspicions but I did a lot of research on this when the film was first released and these were the conclusions I reached. Back then it was nearly impossible to convince people that Michael would've mimed any of the film, and to them I say:
He didn't mime most of this film.
Why would these prerecorded vocals be altered so heavily to fit with Michael's mouth onscreen?
Because these tracks were edited for the purpose of the film, to replace live audio that was once there but for some reason had to be removed.
Don't believe what the editors, Kenny Ortega, ANYBODY says about the vocals being recorded "too quietly." That is a load of garbage. Anybody who is well-versed in recording with high-end equipment knows that is an utter lie. If the vocals were too quiet to be audible over the music, you can go into the mix and increase the volume of the separate vocal track. That is almost definitely how these concerts were recorded, considering they were able to take the original vocals out in the first place.
I am disgusted at how carelessly and guiltlessly these filmmakers lie to their audience.
Almost all of these vocals were recorded live during the rehearsal process, but for some reason Sony and the film editors felt that it was better to replace many of those vocals with previously-recorded ones, likely for quality purposes. For typical audiences, this probably isn't an issue. For the true fan, it's a major problem.
To me, this detracts from the film since it does not show an accurate depiction of the rehearsals. Unfortunately I doubt we will ever see the true live tracks from these rehearsals, since the videos are locked away in a vault with Sony or the MJ Estate.
There are songs not included in the film which we have evidence of having been rehearsed (pictures, amateur audio, set lists) - this includes Dangerous, Stranger in Moscow, and Don't Stop 'Til You Get Enough.
This Is It was a film that could have been absolutely incredible and timeless, but was all but ruined by this over-editing.
End rant.
Some songs are definitely live in the film, I would say these are mostly or entirely live:
Wanna Be Startin' Somethin'/Speechless
(I have a feeling that the style of this particular rendition plus the unique and quality performance Michael puts on pushed the film editors to retain most, if not all of the TII rehearsal vocal)
Human Nature
(The best vocal performance in the entire film, but comparisons with the original Human Nature preview, http://www.youtube.com/watch?v=FsVYuGwAuR0 indicate that the track may have been pitch corrected or otherwise altered)
Jackson 5 Medley
(Michael never really had trouble singing this one, even in the rougher HIStory years - I suppose it is possible that they took this from another live performance, but I doubt it)
I Just Can't Stop Loving You
(The roughness and unique quality of Michael's vocal track here appears to be from the TII rehearsals)
Black or White
(He never would have sang with this kind of falsetto in an actual live performance, so I think this is also from TII)
The following songs have some live portions, but are clearly mixed with previous live or studio vocals:
Smooth Criminal
(listen to the ends of certain verses and most of the chorus vocals)
Man in the Mirror
(the "HOO" section is definitely live)
The Way You Make Me Feel
(the introduction and very end, where the band accidentally stops early, are live - though I have my suspicions that parts of the introduction are taken from other sources)
Beat It
(The "HOOO" intro and some of the shorter "Beat its" in the first chorus, as well as some of the ad lib section, appear to be live vocals, but the rest is almost certainly lifted from another live performance)
These songs are almost entirely prerecorded from a studio or live performance, and you can actually hear how the film editors cut audio in order to fit with the video:
Jam
(The vocals here are at times not quite on the beat with the rest of the band, but it's clearly from the original Dangerous album track)
They Don't Care About Us
(hear the pacing of some of the lines, it's clearly the studio track Michael recorded back in '96 but it has been edited to fit with the video - compare this with the first clip released to news outlets when Michael passed back in June 2009)
Thriller
(is clearly just playback from the album version, nothing special - though the fact that the vocal has not been edited much leads me to believe that this was actually going to be playback in the actual concerts)
Earth Song
(has clearly been lifted from the "What About Us" demo leaked on the Dangerous DAT tape as seen here http://www.youtube.com/watch?v=Fu3M_85aTV0)
Billie Jean
(has been taken from this demo of Billie Jean http://www.youtube.com/watch?v=MGlqlkkryFE or at least a similar demo, which is curious since we have knowledge a live TII rehearsal vocal exists - see this commercial http://www.youtube.com/watch?v=Jnpx42yv7h8)
Now this are just my own suspicions but I did a lot of research on this when the film was first released and these were the conclusions I reached. Back then it was nearly impossible to convince people that Michael would've mimed any of the film, and to them I say:
He didn't mime most of this film.
Why would these prerecorded vocals be altered so heavily to fit with Michael's mouth onscreen?
Because these tracks were edited for the purpose of the film, to replace live audio that was once there but for some reason had to be removed.
Don't believe what the editors, Kenny Ortega, ANYBODY says about the vocals being recorded "too quietly." That is a load of garbage. Anybody who is well-versed in recording with high-end equipment knows that is an utter lie. If the vocals were too quiet to be audible over the music, you can go into the mix and increase the volume of the separate vocal track. That is almost definitely how these concerts were recorded, considering they were able to take the original vocals out in the first place.
I am disgusted at how carelessly and guiltlessly these filmmakers lie to their audience.
Almost all of these vocals were recorded live during the rehearsal process, but for some reason Sony and the film editors felt that it was better to replace many of those vocals with previously-recorded ones, likely for quality purposes. For typical audiences, this probably isn't an issue. For the true fan, it's a major problem.
To me, this detracts from the film since it does not show an accurate depiction of the rehearsals. Unfortunately I doubt we will ever see the true live tracks from these rehearsals, since the videos are locked away in a vault with Sony or the MJ Estate.
There are songs not included in the film which we have evidence of having been rehearsed (pictures, amateur audio, set lists) - this includes Dangerous, Stranger in Moscow, and Don't Stop 'Til You Get Enough.
This Is It was a film that could have been absolutely incredible and timeless, but was all but ruined by this over-editing.
End rant.