Fix Corrupted EndNote Library

Due to the limited space of EndNote online, I still used to sync EndNote libraries through OneNote. The drawback is, the library might be corrupted occasionally (about once a couple of months).

The first I could do is try to recover the corrupted library, follow the instruction in EndNote: The proper process for recovering library files.

But sometimes it could not work and output “0 references were recovered”. How to save the library?

An EndNote library is composed with one “.enl” file and an “.Data” library, the structure may like:

|-- mylib.Data
|   |-- PDF
|   |-- sdb
|       |-- pdb.eni
|       |-- sdb.eni
|-- mylib.enl

The .enl and .eni are SQLite3 databases, and the validity of these files could be checked by SQLiteStudio. In this situation, the “mylib.enl” file might be ok, but index database “.eni” corrupted.

Next simply remove corrupted “.eni” file (or rename, which is safer).

Then try to recover the library as EndNote instruction.

To avoid data loss, frequently backup EndNote library is important. The proper way to backup a library is to create a compressed EndNote library (.enlx), follow the instruction in Backing-up your EndNote Desktop library.