I don't see why they would. That would alienate the millions of people who have embraced Cobra Kai and made it a huge success. Honestly, I wouldn't be surprised if they bring in Chan during the last episode, to create a bridge between the show and the movie.
Word is that, while they are two completely different teams, ie Sony Pictures Television for Cobra Kai, Sony Pictures for the movie, the Cobra Kai team is helping out where they can.
At least according to Dark Horizons.
Dark Horizons said:An update from Gizmodo indicates that while the team behind Netflix’s smash hit “Cobra Kai” aren’t directly involved in the project, they have been involved in the process.
Sony Pictures Television produces “Cobra Kai” for Netflix, whilst Sony Pictures is producing the film. The site indicates the show’s creators Jon Hurwitz, Josh Heald, and Hayden Schlossberg know the film is happening and have offered assistance when asked.
So, that leads me to believe that the movie team knows how the series ends, and that the movie will possibly take off from where it ends. It also seems they're going all-in making sure nothing is being contradicted, either from the Miyagiverse or Jackie Chan's reboot.