I've been working on this book series for quit some time now, and it's pretty much my Magnum Opus. I realize now though, that my first book is quite separated from the rest of the series, as in: My protagonist is a young boy in the first book, and the rest of the series he is older, and almost none of the characters in the first book ever come up again for the entire duration of the series -- rather like Ender's Game is pretty separate from Speaker of the Dead, Xenocide, and Children of the Mind. But even though Card did it that way, I am having real doubts about this. My first book is pretty much just to get me into the rest of the series in some ways, and so I feel like it needs to be either completely redone, so that it has more relevance, or it needs to go completely. It's also sort of like The Hobbit is separate from the LOTR books, in a sense. I get real iffy about revealing too much on here, but I think this will be okay -- The first book is a boy reading about his grandfather's adventures in a journal, and the rest of the series is him on his own adventures. I need some thought, please.
While I cant exactly give in depth advice, since I know nothing of your series. I will say that having a stand alone entry novel is fine. I would keep your current draft if you are attached to it. But if not, then there is no problem with re-writing it to fit with the rest. Either scenario works; so long as it is written well.
i agree theres nothing worng with a stand alone entry novel. if your mc is no longer in say his home town where he read about his grandfather. and as you said time has past and he has left to go on his own adventures so unless these characters followed him on these adventures then theres no real point in haveing them in the rest of the series, unless he returned to his hometown.
Another thought is that maybe you could think of a story to fill the time-skip. But in any case, nothing wrong with the timeskip itself. If that's how your story works out, go for it.