Backup Disk 'doesn’t contain an EFI system partition' I have a 750GB Western Digital external HDD which I use for Time Machine backups (MBP, OS 10.10.3). Today I had the need to boot to recovery, which I did from said backup. But I was unsuccessful in doing it again, whenever I booted with ⌘-R, OSX went straight to internet recovery. I can still boot to recovery from it by holding ⌥ at boot and choosing the disk.

Now, when booting from my internal disk and running a Verify Disk on the backup drive, it says 

Error: This disk doesn’t contain an EFI system partition. If you want to start up your computer with this disk or include it in a RAID set, back up your data and partition this disk.


Meanwhile, running diskutil list reveals

/dev/disk3
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *750.1 GB   disk3
   1:         Microsoft Reserved                         134.2 MB   disk3s1
   2:                        EFI EFI                     209.7 MB   disk3s2
   3:                  Apple_HFS WD                      749.6 GB   disk3s3


I never bothered to check it before, so I do not know if something has changed there, but firstly, I do not know where the Microsoft Reserved partition comes from, or what it is, secondly, I can see the EFI partition, so why does Disk Utility ignore it? And how do I make it useable for recovery without erasing all data?
Unless I'm missing something here it shouldn't be much more complicated than booting into your recovery partition (assuming it's working correctly), reinstalling OS X and then restoring your data from the TM backup on your WD drive when prompted at the end of the OS X installation process.

If you have issues with the recovery partition go for Internet Recovery instead, using Disk Utility to erase your drive before attempting an OS X installation. This will allow the OS X installer to create a new clean recovery partition that should be accessible from CMD + R.

The WD drive should be usable for recovering your data in its present state as Time Machine will alert you the first time you try to use a drive if it has an incompatible file system. As you've made a TM backup the drive must already be correctly formatted. The EFI issue should only really affect you if you are trying to boot from the external drive, which you're not as it doesn't have OS X installed on it. If you've any doubts about your external WD drive then repartition it once you've restored your old data, this should flush out the Microsoft system partition and create a new EFI partition in the correct location on the disk.