but why does it cause the error?
I can imagine that sometimes the EF team regrets the day they introduces this Include syntax. The lambda expressions suggest that any valid linq expression can be used to subtly manipulate the eager loading. But too bad, not so. As I explained here the lambdas only serve as a disguised string argument to the underlying "real" Include method.
how do I fix it?
Best would be to project to another class (say, a DTO)
db.Courses.Select(x => new CourseDto {
Id = x.Id,
Lab = x.Lab,
Modules = x.Modules.Where(m => !m.IsDeleted).Select( m => new ModuleDto {
Moudle = m,
Chapters = x.Chapters.Where(c => c.IsDeleted)
}
}).Single(x => x.Id == id);
but that may be a major modification for you.
Another option is to disable lazy loading and pre-load the non-deleted Modules and Chapters of the course in the context by the Load command. Relationship fixup will fill the right navigation properties. The Include for Lab will work normally.
By the way, there is a change request for this feature.