*** before proceeding, make sure that you have a backup of the hdd/ssd ***
Well it is not clear if the data in the Apple EFI partition is really used by OS X. However assuming that it is used you could mount the EFI partition as shown here.
And then open the EFI partition folder using Finder and take a look at what is there. On my rMBP I found this in the EFI partition folder. And there are three hidden files that I would not worry about.
You may be able to delete all but the files shown in this capture.
OR.... You could back up the partitions to another drive and re-format and re-partition the drive. The restore the data. For example you could use SuperDuper or CCC to clone the partitions off to another drive and run the reverse clone process to restore after the re-format and re-partition.
NOW... if the Macbook won't boot now then you will need to pull the hard drive and use a second machine to make the edits that I have indicated and/or re-build the drive as indicated.
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