MacOS – EFI Partition seems to have been replaced, can still boot with rEFInd but need to repair EFI Partition

Ubuntu has instructions for most macbook pro's. Depending on which version of the macbook pro you have you may not need rEFInd:

https://help.ubuntu.com/community/MacBookPro

Note: El Capitan (OS X 10.11) prevents users from selecting rEFInd and common Linux distributions from the Startup Disk pane. The new preferred method is to install rEFInd into the an EFI partition. My answer, to an unrelated question, outlines this new preferred method to start the rEFInd Boot Manager and Linux operating systems. The answer, given below, applies to Yosemite (OS X 10.10) and possibly earlier versions of OS X.

Personally, I installed rEFInd on my computer to its own partition. This prevents the problems you are encountering. Everything ./install.sh installed went to this partition. If I want to remove rEFInd, I can simply erase or remove the partition. Of course both are unnecessary, because I can turn rEFInd on and off at will. I just go to the Startup window in System Preferences select my boot partition. This computer has OS X, Windows, Fedora and rEFInd installed.

I also can select the boot partition under Windows by using BootCamp and by holding the Option key down at startup. The command diskutil list produces:

/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *500.1 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:                  Apple_HFS Marlin                  300.0 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
   4:       Microsoft Basic Data Coelacanth              98.9 GB    disk0s4
   5:                  Apple_HFS Linux HFS+ ESP          209.7 MB   disk0s5
   6: 0FC63DAF-8483-4772-8E79-3D69D8477DE4               524.3 MB   disk0s6
   7:                  Linux LVM                         98.6 GB    disk0s7
   8:                  Apple_HFS rEFInd                  939.5 MB   disk0s8

Note, the rEFInd partition is ~ 1 GB in size. In fact, it can be as small as 100 MB. When I setup this computer, I used the Disk Utility application to create the rEFInd partition. If I would have used the gpt command, I could have created a smaller partition. Neither OS X, Windows, Fedora nor rEFInd use the EFI partition to boot the computer. In fact, there is nothing useful in the EFI partition.

Answer to your questions:

How do I uninstall rEFInd 0.8-3.7 using OS X 10.10.3? Read the ./install.sh file and undo whatever it did. I should of had you run the commands bless --info and bless --info --getBoot. These would have told where the .efi file was stored. Note: Almost everyone installs rEFInd to the OS X boot partition.

How would I go and reinstall it using different options if I cannot remove it? The author of the software never said rEFInd could not be removed. I suggested you just install it again to its own partition. This might be a good place to mention the gpt command has to be run while either booted to an external recover partition or while booted to internet recovery.

Could I simply remove the EFI partition or would that corrupt my Mac? Do not remove the EFI partition! It is not used to boot OS X, but it is used by OS X for other things.