The car still beeps but it is triggered by pulling off from a standstill or pot holes. If you get going and stay on a smooth straight road it stops beeping
What does that mean? do you mean driving without interfering with roof switch it just starts beeping, and also drives ok [silent] until you hit a pot hole then beeps.
Sounds to me like you have a loose wire somewhere if this is the case, is the roof fixed tightly to the top of the screen in other words has it started to open then given up so it is effectivly closed if you like but not fully locked in place, you could also check around the boot area as if that boot lock plays up a bit it can trigger a roof problem as the roof ECU thinks the boot is not shut, I supose you could ask also is the boot fully shut? I did this with a Vauxhall astra on hols chucked me snorkel in the boot shut it [or thought I did] fired it up no donging went on to warn me but roof failed to work????? temper tantrum time as airport was 2 hours away, but it was the boot lid not shut. worth a look.
Sounds like you have something making an intermitent conection if I have read right, the smooth straight road stops what ever bouncing or twisting so a conection is made beep goes off all systems fine or so car thinks, until a bend or pot hole or a junction so the car shudders, twists or shifts its weight causing the conection to break again. The speed sensor is supose to stop you opening the lid on the move it disables the lifitng gear and bleeps at you but your seems to me to be bleeping indiscriminatly so would sugest a break somewhere and as the roof wont work it seems to be on the roof circuit, I take it the boot blind locating switch is ok, but even then I can not see that setting of the bleeper on the move, it just would not let you open roof end of unless it has as I mentioned allowed you to just start lifitng then packed in so roof is not fully locked on the windscreen.
I can not think where else you would look, boot lock controls roof, I would imagine there are sensors on the reverse lifitng gear for the boot lid as well [when roof comes off boot opens other way] it could be one of them got wet where ever they may be, possibly shorting with water inside, grabing at straws really but maybe two heads better than one with you saying the seals where blocked and boot was full, it had to get there some how but via what? boot floor is where it will end up last, seals are where it first came in where did it go in the middle.
Sorry can not be more help, they are a bit of a mystery these cars as not a lot of info posted on them or googleable either.
Doesn't help when none of the manuals on the Megane cover the CC roof. my Dialogys does not work! another great ebay purchase [NOT], and one I got from another source is in Russian! not much use either.