Journal (Plant, Cell & Environment) output style changed in endnote, but does not change correspondingly in word as it should be.

In my experience the 2007a,b only works if all the authors are exactly the same, not just the first author.  I tend to ignore this as the journal publishing house usually has the tools to make these little adjustments.  I feign ignorance unless they complain, and then I edit the final accepted manuscript to avoid glitches like those you worry about from editing as you go along.