As Leanne suggested, first thing to do is to download update journal name term list.
Then, what Endnote does is, compare the journal name in your database with the term list. If it finds the match, appropriate abbreviation is applied.
Say for example, you have a reference of Journal of Urology in your database downloaded from Pubmed.
If your style uses “Use full journal name” option, then output will be Journal of Urology
If your style uses “Abbreviation 1” option, then output will be J. Urol.
If your style uses “Abbreviation 2” option, then output will be J Urol
If your style uses “Don’t replace” option, then output will be Journal of Urology
Up here is very simple.
In the case your download from Pubmed but the import filter gave you a reference of J Urol , Endnote still searches in the term list, and finds it in the Abbreviation 2 of Journal of Urology. Then all the options work as expected. Confusing thing is some filters give you full name, some give you abbreviated name when you download and import from Pubmed. As long as Endnote finds the name in the journal name term list, it works. So, downloading updated term list is very important. However, if Endnote can’t find the matches anywhere in the term list, then it automatically uses “Don’t replace” option. For example, if you have a reference of World Poultry J , Endnote doesn’t find a match in the term list, and output will be World Poultry J , even you choose “Use full journal name” option in your style. In this case, you need to define the abbreviation for this journal manually in the term list, like World Poultry Journal in full name, World Poultry J. in abbreviation 1, and World Poultry J in abbreviation 2.
Does this make sense to you?
I think your problem is somewhat explained by this.