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This sounds like the issue we have been trying to recreate. I have tried several times, but I am unable to reproduce the issue locally. You seem to be able to recreate the issue pretty consistently, so there must be something I am missing.
If you run the Parser Wizard and save the parser configuration, the log file is refreshed. As part of the refresh process the file is removed and re-added to the view. It seems LogViewPlus is getting confused on the refresh.
After the parser has been configured, are you able to open the file - possibly after a restart? If you are able to open the file, what happens if you refresh it (F5)? Are you opening the file directly or through a Directory Monitor or Workspace? Is there another file with the same name open? Are there any errors in the SFTP transfer log?
Sorry for all of the questions. This is a very strange issue.
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