We can answer precisely none of your questions here. The first three are going to have to be questions for your DM, and the last is something you’re going to have to do your own research on because it’s too broad for a question here.
- When we project, does that body remain as is until AP is dispelled?
Your body is in “suspended animation,” which (in other spells, and in narrative precedent) means time isn’t moving for your body. Astral projection’s use of “indefinitely” to describe how long you can project also suggests a lack of aging.
What’s unclear is whether or not spells effecting that suspended body are also suspended—the rules don’t say. You’ll have to ask your DM.
- Does the duration expire? Or can it be dismissed normally for the protection, returning them to an Incorporeal state?
For personal-range spells, probably not: in order to dismiss a spell, “You must be within range of the spell’s effect,” which isn’t true for a spell on your original body while you, yourself, are an astrally-projected copy of that body.
For spells that could be targeted on others, you definitely have to get your projection within range of your original body to even try it. At that point, though, you’ll have to ask your DM: is it still “your” spell, when you are a “copy” of the one who cast it? Who knows! For that matter, can a spell effect be ended, from the outside, on a creature in “suspended animation”? Unclear! Temporal stasis supplies a bit more detail on what “suspended animation” means (at least for the purposes of that spell), and says “no force or effect can harm” the suspended creature, but is dismissing a spell effect a “harm”?
The rules have answers for none of these questions.
- If the duration is the same for both bodies/the spell is linked to both in some way, when the original body returns to the Mindborn state, does Astral Projection snap you back into that body because it's not a physical body anymore?
This is the question of whether or not 3.5e implements “active targeting,” which has come up before. See the answers to this question for more details. The short answer is, the official rules are silent on this issue, the official FAQ claims that 3.5e does not have constant targeting (so astral projection won’t care if you stop being a legal target), but the FAQ is frequently wrong and near-useless as an authority, so really you’re going to have to ask your DM.
- And finally, is there a better way to do this? Astral Projection is one of the best save-your-life-while-adventuring spells out there and if I can find a way to cheat around the physical body problem I'd really like to.
Many, many, many better ways to accomplish invincibility, if that’s what you mean by “this.” If nothing else, Pun-pun exists as a thing that can be in done in 3.5e, at which point it’s literally impossible to stop you from doing literally anything you want, whenever you want, and astral projection is entirely unnecessary. Trying to list all of them is vastly out of scope for a question on this site, much less a tangential fourth bullet point.
If you instead mean using astral projection specifically, I mean, to begin with, being in “suspended animation” might already be a perfect defense not needing any improvement. Temporal stasis suggests nothing can “harm” you in that state, so what does it matter if you’re incorporeal or not?
Beyond that, frankly I don’t buy that astral projection actually requires you to have a corporeal body in the first place—I simply don’t think it’s good practice to read so much into the descriptions used in 3.5e. When they want a hard restriction like that, they usually write it, so absent that, I think natively-incorporeal should have no problem casting astral projection. For that matter, I’m also not giving 3.5e’s editors credit sufficient to be willing to read “you must cast it from the Material Plane” in between the lines, so you could, in my opinion, cast the spell from some hardened demiplane.
However, since no effect in the game can save you if the silver cord is cut, astral projection seems to me like a poor approach to invincibility, so each of these opinions is largely moot. Note the silver cord is incorporeal without you having to do anything special about it.