In part II on October 21, 2015 at 7:28pm, Doc, Marty, and Jennifer travel back to October 26, 1985 at 9:00pm, without knowing that Biff had recently stolen the time machine and altered the past. Jennifer was unconscious, after fainting when she saw her older self in 2015. Doc and Marty left Jennifer on a porch swing outside her house, and then went to each of their homes. After discovering how Biff had altered the past, Doc and Marty use the DeLorean travel from October 27, 1985 at 2:42am back to November 12, 1955 at 6:00am, and successfully restore the timeline. In part III Marty eventually returns on October 27, 1985 at 11:00am after being stuck in 1885, and goes to Jennifer's porch to wake her up. Jennifer was placed on her porch by Doc and Marty in the timeline where Biff was a millionairre, but what happened once the timeline was restored?
Since Doc, Marty, and Jennifer traveled to October 26, 1985 at 9:00pm, presumably they should still arrive at that time once the timeline has been restored. In the restored timeline, Doc and Marty would return home and everything would appear normal. They would have no reason to travel back in time, so would Doc and Marty simply remain on October 27, 1985 past 2:42am? If that were the case, then there would be two Martys once he returns at 11:00am on October 27, 1985, and there would be a Doc in 1985 in addition to the one that stayed in 1885. When Doc returns in the time machine made from a locomotive, he mentions that he had already been to the future, which means he probably would have discovered if there were two Martys or another one of him, but he doesn't mention either of them having a duplicate. So what happened from October 26, 1985 at 9:00pm until October 27, 1985 at 11:00am?
A theory I've read from other people is that the timeline changed around Jennifer: that to an observer, Jennifer appears from thin air, and to Jennifer, elements from the timeline where Biff is a millionairre will disappear (like the bars on the windows) and other elements will reappear. This is consistent with what Doc says as they are about to travel to November 12, 1955, "Assuming we succeed in our mission this alternate 1985 will be changed back into the real 1985, instantaneously transforming around Jennifer and Einey. Jennifer and Einey will be fine, and will have absolutely no memory of this horrible place." This begs the question, exactly what time does Jennifer appear on the porch? She arrives back on October 26 at 9:00pm, but it takes time for Doc to drive to her house and for Marty and Doc to carry her to the front porch. If she appears some time after Doc and Marty place her on the front porch, why would she appear at that time? The timeline is not going to make her appear at a specific time for the sake of "convenience". Would she appear at 9:00am at the same location as the timeline where Biff is a millionairre, moving down the street as though she were in an invisible car, and then appear to be carried by invisible people to her porch swing?
Also, what would happen if someone (Doc, Marty, Jennifer, Clara, or anyone else) were to use the locomotive Doc and Clara arrived in at the end of part III, travel to October 21, 2015, hide in the DeLorean somewhere when nobody is looking (Biff managed to steal it after all), and travel with Doc, Marty and Jennifer back to October 26, 1985 at 9:00pm? Would they arrive back at the timeline where Biff is a millionairre, or would they arrive in the restored timeline? Would Doc, Marty, Jennifer, and/or the DeLorean disappear once they arrived?
Since Doc, Marty, and Jennifer all traveled back to October 26, 1985 at 9:00pm in the DeLorean, I think it would make the most sense if all of them appeared in the restored timeline. Doc and Marty would then take Jennifer to her porch and return home. Then Doc, Marty and the DeLorean would disappear at 2:42am, rather than for Jennifer to appear from thin air on or after 9:00pm.
A similar issue is that in the timeline where Biff is a millionairre, Marty is at a boarding school in Switzerland and Doc is in an institution. When the Doc and Marty we see in the film arrive back to 1985 from 2015, what happens to the Marty in Switzerland or the Doc in the institution? Do they vanish or do they remain? Would the Doc and Marty we see in the film end up disappearing? Do both Docs and Martys remain? If they both remain, then it seems likely that once they get the almanac from Biff and the timeline is restored, the Doc and Marty that come back from 2015 would remain as well as the Marty that arrived from 1885 and the Doc that remained in 1885.