Disclaimer: I'm the owner of the project Entity Framework Plus
EF+ Query IncludeFilter feature allow filtering related entities. It support EF5
var packageInstanceDB = entity.PackageInstances
.IncludeFilter(x => x.Sessions)
.IncludeFilter(x => x.Sessions.Select(y => y.Notes.Where(sn => !sn.IsDeleted)))
.IncludeFilter(x => x.Sessions.SelectMany(y => y.Notes.Where(sn => !sn.IsDeleted)).Select(z => z.Documents.Where(sn => !sn.IsDeleted)))
.First(p => p.PackageInstanceId == purhcaseSessionId);
Note: Every path must be included
Wiki: EF+ Query IncludeFilter