I've had exactly the same issue, multiple times. Basically the Watchlist and Continue Watching are totally unreliable. I now keep my own record of my Watchlist and Continue Watching because you simply can't rely on NOW to do it reliably
I think this is totally unacceptable and have complained multiple times about it. Generally live chat is useless (and I find that the button simple doesn't work most of the time too), you often get people who are totally ignorant. I was once told on live chat that downloads were stored on the cloud!
You could also try emailing customer services: CustomerServices [at] NowTV.com but you don't always get an answer there either.
Basically it's all a mess. I only stay with NOW because you can watch Sky programs and it's cheaper and you don't need dedicated hardware.
The lack of profiles really just grinds my gears also!
Whereas this isn't a problem to me personally (I'm the only person using my account), I get that it is a very serious limitation to households with multiple users. It makes the Boost feature of using multiple devices at the same time virtually useless.