How can I troubleshoot why suddenly 8 of 10 subfolders with proxy logs have stopped being indexed?

I've been sending proxy logs to the FTP server and from there I installed an universal forwarder to send the logs to the Splunk indexers. They are all in a gz format. Everything was working fine until a day when I've noticed that proxy logs stopped getting indexed. There are about 10 subfolders and only 2 of them are still getting indexed, and the rest of the proxy logs had stopped getting indexed on the same day. How should I troubleshoot this? Not sure why some of the subfolders with gz files (proxy logs from each site) has stopped getting indexed and the rest is still going.