In refman you have the opportunity to merge term lists. For example I have a journal named Am. J. Cardiol. and another journal Am J Cardiol in the journal term list. I then want to merge them into one, but the only way I can handle is to change one of them globally, and then manually for the other term change the journal for each occurrence. That is a cumbersome process, and in Refman it was simple to merge two terms and then change them all to the proper value
If they aren’t recognizing the same “term” in the Journal term list, just add one of them to the 3rd or 4th column. Endnote will make the conversion in your bibliography, just fine.
I agree with jkanters. Until recently, I was using Ref Man, but all my students are using EndNote because they can get it for $99 academic discount. So I switched.
After downloading references from Web of Science and Elsevier and other sources, I get journals in odd formats (e.g., all caps) and keywords I don’t want. If this happened in Ref Man, I could merge the incorrect journal name with the correct one and merge the undwanted keywords with ones I already have. Can’t do this in Endnote. The suggestion just above for Endnote is cumbersome (as jkanters wrote) compared to what RefMan can do.