Just had this happen to my MBP 2015 Retina. This is something that everyone should be very aware of. It can happen really quickly even by accident. I was consolidating and cleaning out a few external hard drives I had around. One of them I had used several months ago for a hackintosh build install, so it had clover in its EFI. I had reformatted the main partition, but did not realize the EFI was still intact with clover ready to boot. I also use reEFIt as a standard boot loader so when the menu came up I didnt think twice about pressing enter in to Mac OS. I realized after that it was loading from clover but did not think much of it. Everything seemed to work fine until I decided to restart. On the next boot it is stuck at the chime and does a restart loop before the chime even finishes.
Talk about a panic! It took me a minute to figure out after searching online that clover was the culprit and that the EFI in the logic board is corrupted. Not good news!!
I will be ordering the macunlock EFI first chance I get. Very fortunate to know that there is a solution to fix this that is relatively simple. I will post a follow up as soon as I receive it.
P.S. Not sure if this is already, but maybe this thread should be a sticky. This is a very serious situation that should have more awareness. Mac users beware of clover!