I’m not familar with Modded Minecraft server issues, so will let someone else step in to see if they can assist. I would recommend searching the forums though as there have been a lot of modded Minecraft issues resolved.
One in particular you might look at is Restore backup on new server - #15 by Daniel_Ertl It doesn’t deal with Minecraft but there were some other files people had to restore to get good backups running.