I have read all the treads on this topic, followed the advice previously given by the forum, but problem remains.
On Sunday being a nice sunny day went for brunch at second favorite waterside restaurant. Top down, 30 minute drive, park, top closed, then breakfast.
Came out started car, started to put top down, stopped part way (my finger may of slipped off button!) would not go down despite several presses, so pressed the up or close button, top went up and, I thought latched, but then the rear quarters did not come up and the dreaded "Hood Not Latched " appeared on dash!! No luck with either pushing down button nor top up button. Top appeared to be firmly latched so drove home cautiously with top up.
After reading all the advice, did multiple main window resets, pulled fuse F8 for 15 secs, 1 minute, 30 minutes, still no luck. Fluid was at the minimum line, so bought new CHF 11S spec fluid, sucked out old fluid as it appeared quite dark compared to the fresh fluid, filled to between mid way and maximum marks.
So to the manual Convertible Top reset. Unwind pump from auto to manual about 1 &1/2 turns. Had to unwind top latch about 20 turns to get the top tpo release after waiting the 30 mins to let the pressure subside. A few mis-steps while doing this for the first time, but got it packed away and tonneau cover appeared to be latched. Closed off the pump to auto. closed the boot/trunk. Fired up and the dreaded "Hood Not Latched " was still there, but hitting the top button, up it came, the dash cleared to the clock, and then the top stopped about 4" (10mm) from the windscreen , and "Hood Not Latched " came up again.
Several repeated attempts produce the same result, window reset, remove fuse F8 with top down all not improving things.

Where do I go from here?

 

Try holding the button in the down position for 90 seconds. I have had that work a time or two.

 

[QUOTE=JackJohn;2568416]Try holding the button in the down position for 90 seconds. I have had that work a time or two.[/QUOTE

Agree, had same thing happen to me.

 

Thank you for the guys that replied and those who threads' I researched . I HOPE it has been RESOLVED.
My observations;

1. As I had been trying all sorts of things over the previous days, I checked the battery voltage and it was 12.3V, so put it on charge for several hours.
2. This morning it was 13.1V.
3. The tonneau cover immediately after a manual lower did not sit flat, about 12mm (1/2") proud. Pushing it down did not latch and sprang up again. I left the pump in manual mode overnight
4. This morning tonneau cover was flat across the shut line.
5. Put pump into "auto" mode.
6. Started car, "Hood Not Latched " came up, tried the 90 second lower as suggested, no luck with two attempts.
7. Turned car off. Removed fuse F8 from between rear seats left for about a minute, then put it back in.
8. Started car, "Hood Not Latched " came up, tried the lower button, and then "click" from under tonneau cover, no alarm message on dash, but I kept pressing "lower" for the full 90 seconds.
9. Pressed "raise" up the top went, rear quarter windows up, then main windows up and confirmation ping!, two very happy people!!!
10. Main windows auto up and down worked first try, without doing the window reset, but I did it anyway.

THANKS TO FORUM

 

I was in the same predictament yesterday while picking up my vechicle after having it repainted. Went through the steps the first time with no sucess, so I closed the top , and used the allen wrench and closed the top's latch.. After that I unlatched it again and folded it back into the compartment. Set everything back to normal, crossed my fingers and everything functioned properply.

I'm thinking manually latching the top at the front and manually runing it through all the open close staisfied the logic of all the sensors and allowed it to function correctly.

I can not be absolutely sure this is the case but it seem to have worked out for me or I just got lucky. If nothing else it may be something to try.

When I had my 05MY and had to replace all the hydraulics and pistions I had lots of issues getting it all locgically working, and the one of the rear window motors went out, sort of never ending at times.

Now I have to move on to the TPMS since there is a fault in that system, I'm still on the originally wheel transmitters and their batteries.
Still have a lot of tire treads left so not really wanting to break the tires down to replace at this point in time.
May have to take it to the dealer and have them trouble shoot and find the exact fault.
Any ideas on how th "disarm" the system?