This error means that the system cannot find a configuration value for this setting for those files. Most likely something irregular happened regarding the default conf files as they are perceived in memory, and wiping the log dir forced splunk to re-consider the splunk-specific logfiles. When tailing starts working on a file, it computes the configurations to use. In this case, an expected setting was not available or was set to blank, and you got a error.
One possibility is that you upgraded from a version that does not have detect_trailing_nulls support, to a version that does, but reinstated the conf files from the older version.
This message is emitted as an ERROR because it indicates that the conf files being used are not in a valid state. However, this specific setting being missing will not affect behavior, as the message states, because it is assuming the default of false and proceeding.
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