I have been using FNV plugin utility to merge new objects into my resource Master file. Since the GECK update the utility no longer works.

Is there another simple way to merge ESPs into my ESM?

I tried merging with FNVedit between version 1 and 2 of my resource, this caused major problems and incompatibilities.
Objects in mods would be replaced with other objects, likely a problem with shuffling form IDs. I can't have this problem with version 3 or several popular mods will no longer work with the new version.