Journal abbreviations and BibTeX drive me nuts. Some journals demand that you submit manuscripts with abbreviated journal titles in the bibliography, while others want fully spelled-out names. The only solution that I’m aware of is to keep two .bib files, one with abbreviate names and one without. However, this means keeping two .bib files up to date, and I don’t know how people do that without tearing their hair out. This got so annoying that I finally wrote a Python script to use the JabRef abbreviations lists to flip back and forth as needed. That way, I can keep one master .bib file and abbreviate it when I need to.
The results aren’t always perfect, but they do cut out 90+% of the find-and-replace work needed to handle a journal that asks for abbreviate titles. If you need that too, you can download the package from pypi, or grab it from my GitHub repo. Fixes and feature additions are welcome, so feel free to fork it and send a pull request!