No theres only one investigation ..Portugal with support from Uk and Germany....From what I understand after the rape trial all three forces have jurisdiction.
I don't think there can be the slightest doubt about co-operation between these three police forces and who knows what other agencies may be involved. In my opinion they are acting as far as is possible as one on Madeleine's investigation.
The only fly in the ointment appears to be Amaral's less than helpful recent interjections ... but at least he now seems to be keeping quiet for the time being. I wonder if it is slowly dawning on him that the comparisons between the path in which he directed his investigation is being compared with a far more realistic one being followed now. But which was there in the files right from the beginning in one of the first pieces of real evidence recorded and therefore one of the first pieces of evidence Amaral's investigation ignored.