The file you are concerned with is a DB2 Transaction Log file. The error indicates that the log file was in use at the time the db2loggr process was trying to write to it. The only process on the server that should be accessing this file is the db2 instance id. It seems that this file might have been accessed by an OS process (such as an OS backup)
These DB2 LOG files are routinely archived and/or deleted depending on if DB2 is using LOGRETAIN or Circular Logging - which is why you don't see the file any longer.
