Попробуйте выполнить два отдельных шага:
// create a Dictionary / Set / Collection fids first
var fids = (from fb in FooBar
where fb.BarID = 1000
select new { fooID = fb.FooID, barID = fb.BarID })
.ToDictionary(x => x.fooID, x => x.barID);
from f in Foo
where fids.HasKey(f.FooId)
select f