I'm trying to figure out how to work around the error you are getting. Don't open PR. But it has to be able to "see" the old sequence to open or you appear to get the error. Given the error, I'm not sure you can use the old project.
The alternative is to start a new Encore project (use a new name), and use the old transcodes and menus to rebuild the project.
Just "import as menu" the menus from the old directory structure, and "import as timeline" the old m2v/a3c.
Yes, you must redo all the navigation.