A note for Brian K and Terabyte Support:
We have a client who has recently upgraded to Windows 10 586 1511.
He uses BootIT BM with limit primaries turned off, however there were only three actual partitions on the disk:
BootIT BM, Windows 10 and a Data Partition following that. The rest was free space.
He used to have other partitions when he used Windows 7 and Windows 8, but these have since been deleted.
The 1511 upgrade shrank the Windows 10 partition ny 450 Mb and inserted a 450 Mb Recovery Partition between Windows 10 and the Data partition.
The system reboots showing no errors in BootIT BM or In Windows 10.
Having moved the WinRE back into the main Windows 10 partition, he has deleted the 450Mb Recovery Partition. BootIT BM reports this correctly as 450Mb free space.
My surmise is that providing that there are less than 4 partitions, (as in standard MBR), the Windows 10 1511 upgrade does not cause a problem, even when the EMBR is present, (limit primaries turned off).
The situation I reported in my earlier post was when there were more than 4 primary partitions on the disk, the Windows 1511 upgrade attempts the shrink, writes the 450Mb Recovery Partition, which it fails to do and trashes the partition following that.
I still cannot believe that MS have been so stupid in not coding this so that it checks the MBR table correctly. However I am probably being very naive!