Answer
Check for a file named CONNECT_SERVER<n>_<READER_NAME>_problem_files.xml under <IFS_HOME>\instance\<INSTANCE_NAME>\logs — this file tracks files the reader had trouble processing, and if it becomes corrupted, the reader can fail to even start up correctly, throwing this NullPointerException on every attempt. Stop the Connect Server, back up and remove that specific problem-files XML file, then restart the Connect Server — this regenerates a fresh tracking file and allows the reader to resume processing files in its IN folder normally.