I guess the first question that should be asked is what “new” version of KiCad are your using? I had a similar case with an older project. It was discussed here and resulted in a bug report. Supposedly it has been fixed, so if you download a fresh nightly built everything should work. The other option would be to copy your project into a separate folder and delete EVERYTHING except for your project file, schematics files and PCB files and then try to open that new project again. I would personally first go to EEschema and remove all the libraries and add again only the ones you are using, to simplify troubleshooting.