I started using JabRef a few days ago, and I’m not sure if I’m using it correctly—I’d really appreciate your help. I’m trying to merge multiple .bib files that contain many duplicates with slightly different citation keys.
For example, I want to keep the citation key from the imported library:
by clicking on “li2023FTworkflowSched”, which I prefer over “Li2023”.
Then, I press “Keep merged” and “save all”.
Not only the merged entry is not applied as requested, but JabRef keeps unexpectedly changing the citation key of other entries in an erratic manner—sometimes just one entry is affected, while other times it changes all of them—and I can’t figure out why (but it seems to depend on which “save” button I use). Honestly, it’s taking more time than manually copying the entries.
There is an option in the preferences, “Overwrite existing citation keys” and “Autogenerate citation keys”
For importing stuff, there is another option under “Web search”
If I may give a suggestion, you should clarify the difference between “importing” a library and “loading” a library. The latter does not seem to be affected by the overwrite option, which honestly should be disabled by default, if I may (unless you are actually building a new library from scratch). But I’m not sure about that either, I’ll have to rebuild the whole library to be sure
The pattern in your example is probably too complex to reproduce automatically, and I presume that you need to restore the original keys exactly as they were. Otherwise, I would suggest regenerating the keys after deduplicating the library. For future reference, JabRef has very flexible options for key-generation and file-naming options, which you might appreciate (documentation).
There are definitely ways of merging citation keys that would be easier than manually copying entries. I can help if you haven’t dealt with this another way by now.
I’m trying to merge multiple 
