PatternLayout trims the event timestamp down to milliseconds precision irrespective of the configured pattern.

For instance the following config:

<appender name="LOGBACK" class="ch.qos.logback.core.ConsoleAppender">
   <encoder>
      <pattern>%date{dd-MM-yyyy'T'HH:mm:ss.n} - %msg%n</pattern>
   </encoder>
</appender> 

produces output like the following:

13-08-2022T16:05:49.211000000 - A sample log message (0)
13-08-2022T16:05:49.213000000 - A sample log message (1)
13-08-2022T16:05:49.213000000 - A sample log message (2)
13-08-2022T16:05:49.213000000 - A sample log message (3)
13-08-2022T16:05:49.213000000 - A sample log message (4)
13-08-2022T16:05:49.213000000 - A sample log message (5)

As you can see although the pattern asks for nanoseconds after the seconds only the millis are actually output with the nano parts set to zero.

A quick look at the code reveals that the DateConverter gets the timestamp from the ILoggingEvent by calling ILoggingEvent#getTimeStamp() which gives the timestamp in millis instead of the new ILoggingEvent#getInstant().

See https://github.com/qos-ch/logback/blob/master/logback-classic/src/main/java/ch/qos/logback/classic/pattern/DateConverter.java#L59-L62.