I'm sharing so that hopefully the folks who know more than I can chime and provide advice on how to avoid the situation I found myself in, and perhaps save me and some other the grief. Also it might provide some hope in that I ultimately (knock wood) got everything squared away. The TLR version: My battery died, and I got the "convertible top not latched" message. What I'm hoping for as far as guidance:

1) The wisdom on here is to do the "manual top reset" procedure per the owner's manual when one gets the "convertible top not latched" message, which appears to have been necessary and to be necessary every time the battery is disconnected---but do you have to manually drop the top if you started out in the closed position (as I did)? What if it's already down, do you have to raise it, disconnect the pump, and manually lower it?

2) If you know you want to replace the battery, is there a) a way to avoid losing the settings by powering the car through a tender on the positive terminal (as I saw someone do in a video)--or is that a bad idea, and if not, can you do it via the terminal that's in the panel near the taillights, and b) are you better off starting with the top stowed (if your battery has not given up the ghost yet), and if so, c) do you still have to do the manual reset by then closing the top, latching with the tool, and then stowing if you do have to disconnect the battery and lose power completely?

3) (Spoiler alert): The last step I took before it started working again, was to disconnect / disable the hydraulic pump by using the Allen wrench turning it anti-clockwise a turn and a half, and then back. Prior to that I'd run all the steps for the manual reset (more than once) and it was to the point where the pump sounded like it was trying to lift but wouldn't. Did that final action bleed the pump line, or was it just that in all my times connecting and disconnecting the pump, that I hadn't gotten the valve in the right position?

The long version:
I had the battery die on my 2007 XK convertible, there was a ticking noise emanating from somewhere under the hood (or so I thought), and eventually that stopped and the car had no power at all. Perhaps my door wasn't closed and the interior light was on; ironically I had just waxed it the day before and was admiring how good it looked. Anyway, the battery was only six months old, as I'd had to replace it right before I brought it in to have the convertible top worked on by an interior / top shop. I had experienced a leak about six months prior, and initially I thought I'd try to find the culprit line and replace as necessary with new from Top Hydraulics. The video looked like it could be doable. But in the end, after looking into it for a bit and seeing if I could get the part out, I gave up. The shop had the car for about two months, and it's been fine since, they did get a couple of lines that were leaking replaced with the better quality ones from Top Hydraulics. The work was not cheap, but the top was working fine.

After putting in the new battery, I followed the instructions on resetting the windows (or thought I did), but still got the message, so ultimately I figured I had to do the manual reset procedure. Since the top was up, I had first tried to use the tool to close it "more," which may have been my first mistake. I can't now remember for certain if the top would start to retract or not using the button, but I next attempted the manual top reset procedure, disconnecting the pump and lowering the top, the tonneau however would not latch shut, and still the same message. Reading through the threads on here, I pulled fuse F8, disconnected the battery again, reset the windows and brake, and removed the luggage blind (it may not have been seated properly). At one point I got no response at all from the pump. Finally, after the second or third reset and moving the luggage blind bar, I got the tonneau to latch. And no latch message.

But the top would not go up. It started to raise the tonneau, but stopped. It would latch closed with the "down" button, but would not come up. The third time, it barely moved. I thought perhaps the pump needed more fluid, or somehow to be bled. I used the Allen wrench one more time (I am not clear if the "connected" position is all the way home clockwise or not, or if it's supposed to be not quite all the way, the manual is not clear on that), and turned it one and a half turns anti-clockwise, then back. Finally, the top went up and down, and seems to be back to normal. So in the end perseverance (or stubbornness) paid off. But attempting to do the manual reset multiple times (or honestly, even once) is a drag. So my takeaways are to remember the importance of making sure the luggage bar is seated, doing the window reset is necessary per the manual and threads, and the latching of the tonneau seemed to happen only after I re-seated the luggage bar. But I would rather not have to do the manual reset next time, if possible, so I think I'd try attaching my tender to the positive terminal (maybe the one behind the vent) to avoid this, assuming I was replacing the battery before it fully died. If that's a bad idea, (such as, I could fry the electronics or myself), somebody please let me know. A video I saw of a guy attaching a "jump box" to the terminal that actually goes to the battery inspired me to try that if I need to).

I love my XK, but this level of frustration on top of the bill for the line repairs, made me briefly regret not getting the closed coupe version. Can't beat it on a nice day with the top down though.

 

I’ve disconnected the battery several times, and had it replaced once (probably time to do it again), and never had a top problem.
You can only access the battery with the top up, so make sure it’s fully closed before disconnecting.
I’ve only had to do the window reset after reconnecting the battery. Everything else was fine (don’t know about the seat memory, as I’m the only driver, and don’t need to move the seats).

 

It didn't even occur to me that one couldn't access the battery with the top down, but of course you're right. Such an awkward place for it, the coupe owners have it much easier.