I've been to Japan many times but usually on pre-booked business travel, so I'm a rookie traveler when it comes to booking my own stuff. I'm going to Hikone in 3 weeks. My colleagues there said that there are no hotels available anywhere in Hikone, and the closest thing is in Kusatsu (nearly 50min by train) which they booked me for the whole week.

However I was able to book Comfort Hotel Hikone (right at Hikone station) on Japanican for all but 1 day of my stay. I got the confirmation by Japanican in my email, and when I follow the link, the Japanican website says "confirmed".

I heard that booking though third-party sites is risky. Is there any chance I get to the hotel and they say I don't have a reservation? What should be my confidence level?

If I don't trust the Japanican reservation, I can actually book a shorter stay for the same week on choicehotels.com, which I assume is the official website.

Now I have to decide whether to keep the Kusatsu reservation which i'm 100% confident in, or cancel it and bank on the Japanican reservation, or do a combo, but I would rather keep the longer stay I can find on Japanican so I'm not sure if I should drop my Japanican for a shorter stay just because it's the official website.