On the other hand, if they put Ruby and Chomper in a movie, they will have to try and explain who Ruby is and why Chomper is in the Great Valley for all the people who saw the films but never saw the TV Series. And, they never have explained how Chomper got into the Great Valley, even in the TV Series.
I remember asking if Ahsoka Tano should ever be in a Star Wars Episode VII (I'd asked this before they announced that they were indeed making one) and somebody said that it would be odd if she turned up as nobody who hasn't seen the Star Wars the Clone Wars TV Series would know who the heck she was. It would be the same with Ruby, unless they do some explaining, in Journey of the Heart. Chomper, we've seen in movies before, though he'd have to be explained too, as he wasn't even explained in the TV Series as to how he got allowed in.
They can use a cop out by saying that Journey of the Heart came before the TV Series. However, they're going to have to go back to the TV Series at some point or try and bring Chomper and Ruby in and explain about them to the non-TV Series viewers.
The franchise itself is still in doubt. If they dodge this important issue, it could spell the end of it.
With Star Wars the Clone Wars, I think, they cleaned up enough with the reason for Ahsoka leaving and why she's not in Episode III, as being Anakin's Padawan, she should be if something hadn't happened. I'd been wondering, till then, if they were going to do a Revenge of the Sith remake with her and maybe Ventress in it. As it is, they cleaned up the Clone Wars series pretty well. (Wish we knew what happened to Ventress, but, oh well.)
For those who don't know what I'm talking about, Star Wars the Clone Wars was a TV Series (actually, there were two of them, though I'm talking about the 3D one) that takes place between Attack of the Clones and Revenge of the Sith. Anakin gets a Padawan named Ahsoka and she isn't in Episode III, which created a huge plothole that needed to be resolved as she wasn't mentioned as having died (Anakin only mentioned his mother's loss, not Ahsoka's). She wasn't on the list of Jedi who'd left the Jedi Order. Luckily, the last episode of Season 5 of the series explained where she went good enough and that plothole is gone and it actually, no doubt, made Anakin mistrust the Jedi Council more, which furthers the plot of Revenge of the Sith. If they hand't dealt with her, it would have left a need to do a remake of Episode III with her in it. If they didn't do that, Star Wars would have a gaping plothole. (Not that there isn't one already as Sidious refers to Luke as "the son of Skywalker" instead of "your son" in Episode V and also the term "Sith" isn't used in the OT.)
You don't just leave a TV Series dangling when you're making movies too that could go around the same time frame as the TV Series. Ignoring these things you've done in the TV Series when you make a movie can very well tick off those who have seen the TV Series and see your plot hole in the new film and it could well affect the reception of your new film. Universal has to consider that too. Loads of people were ticked about Bron's absence for the first 9 films. If Chomper and Ruby suddenly disappear, it's gonna create a backlash. On the other hand, if they suddenly appear in the movie, it could also create a backlash of confusion from those who have seen the films but not the TV Series.
In short, it could affect marketing negatively either way unless they can bring them in to please those who have seen the TV Series but do enough explanation in the films to satisfy those who haven't seen the TV Series (and maybe even actually get them to see it, which will mean more sales.).