On the new version, 100 days is the maximum value for both Save Cursor Position and Save Bookmarks options. This was to prevent file history from becoming too large.
The bookmark and cursor position info is stored in %APPDATA%\Emurasoft\EmEditor\Common\FileAttr.bin.
If you make automatic backups (using TotalCommander), you should restore the files (or move the files to original drive/location) before opening the files to see bookmarks.