Journal name format when importing from pubmed

We have a large database (> 6000 records) which has been built up by multiple users over many years. I’ve recently realised that for many journals, we have multiple versions of the journal name with different punctuation, e.g.

J Am Coll Cardiol


J Am.Coll. Cardiol.

So far this hasn’t caused any problems, as when creating a bibliography, RefMan seems to be able to handle removing the full stop and replacing it with a space. However I have recently converted the database to EndNote which doesn’t seem to able to cope with the odd punctuation (it removes the full stop, but then there is no space between the words.

I have started manually cleaning up the term list in RefMan (which solves the problem, but is quite time consuming). But how do I stop it happening. No matter how I do it, when I import from PubMed, I end up with journal names with odd punctuation. I have tried using the internet search funtion in RefMan, I’ve tried exporting from PubMed and then importing the text file (with PubMed filter or with Medline filter). Am I missing something?

What would happen if I deleted the current term list and replaced it. Would all my 6000+ refs find the currect journal name?

My company are switching to EndNote in a couple of months and we need to have a clean RefMan library which is compatible with EndNote by then.