Suppose you want to merge two bib files (f1.bib and f2.bib) that have considerable overlap. One easy solution using Jabref works as described below.
Suppose the target bibliography file without duplicates is merge.bib.
1. Copy f1.bib to merge.bib [cp f1.bib merge.bib]
2. Open merge.bib with Jabref
3. Then click File > Import into current database and select the other file [f2.bib]
4. You get a dialog box which allows you to manually decide what entries/versions you want to retain. If both f1.bib and f2.bib are of comparable quality, you can select "Deselect all duplicates" which automatically unselects duplicated entries.
5. Hit "OK" and save the modfied database [Ctrl-S]
