I have some questions. I was looking at the line art of the VF-1 from Macross 2036 and I understand that Macross 2036 takes place in the Macross II timeline.
Ah, yes... and that would make answering this a job for me.

How long was the VF-1 in service in the Macross II timeline? Just looking at the line art from 2036 the VF-1 just looks different. like the gunpod,head,and Fast Packs.
's a question that, unfortunately, doesn't have a precise answer. It's worth noting that the VF-1 Valkyrie has a somewhat different development history in
Macross II's continuity than it does in the main timeline. The variant seen in the TV series with the rounder hands and traditional HUD simply never existed, and the DYRL version is the way it always was. There's also some interesting shenanigans regarding the existence of the VF-1D and a reason for why the VF-1J was the only one to equip armored packs that's since been parroted by Master File's VF-1 Vol.2. It's also worth noting that the VF-1 variants you saw art for from
Macross 2036 aren't just variants of the VF-1, but rather a major upgrade/modernization of the VF-1 platform kinda like the main continuity's VF-1X.
Depending on whether you want to count the VF-1R/VF-1改 in with the original VF-1 or count it as a separate craft, the answer to your question's different. By all accounts, the VF-1R/VF-1改 entered service in the 2030s, and then presumably remained in service (along with a similarly-enhanced version of the VF-4 Siren) until the 2060s and the introduction of the VF-XX Zentradi Valkyrie.
Is there a place with the alternate Macross II timeline? Chronicling the events between DYRL and Macross II?
Yes and no... there's a "VF History" piece in B-Club magazine (Vol.79) that serves as an overview of the M2 parallel world continuity, and there was an inaccurate timeline sheet printed for
Macross II in Chronicle, but I'm not really aware of any one source that completely chronicles the events between DYRL and
Macross II in much detail. As you probably guessed, I've translated it myself, but my plans to get my
Macross II site finished were derailed slightly by my day job and the influx of the new material in Chronicle and a few other rare sources I've since turned up.