http://tesnexus.com/downloads/file.php?id=8665 has a "Merge Plugins" function. Try that and see if it works. Back up your plugins first, just in case.
TES4Gecko merges on a whole file basis. To get around that, first use the display/copy option on one .esp to extract all the abilities to clipboard and save the clipboard as a new .esp before merging that new .esp with your other one.
http://cs.elderscrolls.com/constwiki/index.php/TESsnip
is another option, but is a bit more messy and less user friendly. Works well in those cases when nothing else does though.