I have this issue, seems to have come with one of the last updates as I never had this issue before and I have been using Opera since 2001. I have used multiple monitors for at least 3 years now. But only within the last month or two have I had this issue where some Opera windows just seem to be outside any of my 3 screens.
I have been trying some of the solutions suggested here, but I also use DisplayFusion to have different backgrounds on each monitor and it has some pretty useful options like moving all windows to the current screen. This worked for 2 of my windows but I have 6 open windows and one of them simply refuses to get back onto any screen even with these solutions where I can move one or all windows to the current screen.
I hope Opera rolls out a fix for this soon as its very annoying. I do have one solution that works but I just do not like it. That is to use TabHamster a browser plugin that helps manage tabs, it remembers what tabs you have open from day to day and you can save certain tab configurations. I usually have at least 50 tabs open, probably easily more than 100 tabs on a normal day. Then sometimes I finish with a window that has certain tabs regarding some project I was working on with information related to that and save that windows tabs to a tab group in tab hamster, if I plan on continuing on that later.
But because of this, I have TabHamster remember the tabs that are hidden in the offscreen window, so I can open a new window and use tab hamster to open all the tabs from that window in the new window and then close the old window. Pretty tedious solution, but until Opera fixes this issue, that is the best I can do.
This issue has gotten me to consider looking for a way to ctrl-tab the same way you can in Opera in some other browser, because this is highly annoying. I use Opera to save time and now I have spent probably an hour or two trying to solve this issue in some efficient way and I still have not found any good solution.