This is a problem introduced by
HBASE-13825 where we change the exception type in catch block in readNext method of ProtobufLogReader.
Here if the inputStream throws an IOException due to timeout or something, we just convert it to an EOFException and at the bottom of this method, we ignore EOFException and return false. This cause the upper layer think we reach the end of file. So when replaying we will treat the HDFS timeout error as a normal end of file and cause data loss.