Upgrade broke my Directories

Server Version#:1.16.5.1552-8e8d0c785
Player Version#:

My Synology NAS (DS1819+) told me I could upgrade my Plex server. I did so, and the upgrade apparently damaged my directories, as the contents could be seen, but the files could not be located. I then attempted to rebuild the directories, deleting the old ones and creating new ones. However, the Plex Server now cannot see down to the level of my movies or TV shows when I use the Browse function to set up the directories (these folders are only 1 level down). I have tried typing in the correct path, but the server sees no content. What can I do to fix this?