You can check it by trying to download the table of contents on this page:
Just filter for files that contain "refwork".
Links for children of "Physics Subjects" are not working properly.
The links I clicked were General Information, Authors, Article Titles, Introductory Articles, Physics Subjects, Related Mathematics Subjects.
I used the latest 5.9 SR1 version.
After you finish downloading the project start it again (with "Do not download existing files" option). OEE will try to download the links that it messed up. They all will be error pages.
Replace the old version of oe.exe file with this one.
1000 files is not a problem for a folder, but several thousand files with long filenames really overload a folder on FAT32 drives, so addition of other files becomes impossible.
NTFS cannot be overloaded this way, but 10,000-20,000 files in a folder cause it to be very slow when accessing it.