A very old reason for a problem like this is if the \id lines (the first line at the top of each book) have been edited and no longer match the information in Project properties. An id line for Matthew, for example should look like this:
\id MAT – Full name of project
Teams sometimes change MAT from the paratext code for Matthew to their own language name, like Matiyu. And they sometime change the project name also. Changing the book code causes the biggest problems. All the \id lines should be identical except for the book code matching Paratext’s code.