Let me make it clearer.
The file pdf_index.MYD is too large (more than 200 MB) when synchronizing files, but actually the library is modified only a little such as adding a reference with one pdf file. So I suggest that pdf_index.MYD can be divided into a head file and several data files, and each file is no larger than 10 MB. When endnote is running, all these files are loaded into memory, and when endnote is closed only the head file and the last data file need modification.