If the server running VDV File Converter shuts down unexpectedly then the configurations can be lost. The good news is that VDV File Converter takes a backup of the configuration every day. So the process is to grab the backup .ini file and replace the corrupted one.
1) shut down VDV File Converter
2) Navigate to VDV_File_Converter\data\backup which contains a backup of the configuration files.
3) Open the latest file and see if it contains all the lines/files you are converting.
4) If it is empty, continue to open the files until you find one that has all of your lines in it (start with the newest file).
5) Rename this file and remove the date at the end. You should have a file called vdv_convert_files.ini
6) Finally move this file to VDV_File_Converter\data and replace the old one.
7) Start VDV file converter
Now you should see all of the files that were being converted.