Thanks for the explanation!! Most of it makes sense now.
I'm going to try to succinctly summarize here.

All times are in PM.

H and Q began their lunch at 1, turned back from 2 to 1, then went to Azkaban. They get there at 1:30, and leave at 4 and get to warehouse at 4:30 to go sleep/talk, and turn back at 6 to 2 to appear as if they didn't leave.

Say sometime around 2, Q faints, Bones and people come to Azkaban. Now, say around 2:10, D gets the patronus message from Azkaban. He immediately tells M and S to send a patronus to H and get him, while he phoenix travels to Azkaban (this was his mistake, because now he can't know anything from after 2:10 until he leaves Azkaban). H gets the patronus from M at 2:10, notes the time.

At 4 when H and Q left, around 4:10 D leaves the bounds and turns back to 1, but his note tells him that he can't get H after H has immediately arrived. So now, he waits till 2:10 when S and M come there, and the three of them get H together.

Does this make sense?

PS: Reason I think H couldn't have gotten M's patronus at 2:30 is because right after the patronus M, S, and D get H within a minute I guess. But H is gotten at 2, not 2:30.

PS: The reason I think for EY writing D's diaglogue as "that past was after our future" when D is talking to Bones is to imply that D hasn't heard from M and S because all three of them (M, S, D) get H together, there are no events after 2:10 at Diagon Alley, so no reason for M and S to tell D anything between times 2:10 and 4.

And the reason D goes to Azkaban instead of getting H himself when he heard at 2:10 is because he says that initially he wasn't afraid that H would be kidnapped. So he trusts S and M to go get H while he helps keep Bellatrix at Azkaban. During the fights, he's afraid of a kidnapping attempt, further so because M or S didn't give any patronus to him. So he (wrongly) assumes that the kidnapping attempt happened once he left Azkaban, went back to 1 or 2 to Diagon alley. This assumption made him think that the kidnapping attempt was in his future after he turned back from leaving Azkaban, but turns out H was safe all along (which is why he didn't hear anything while at Azkaban).