I would use two separate loggers that make use of different appenders that write to the same file name. For example, here would be my conf:

                 Log::Log4perl Conf

log4perl.logger.my_app = DEBUG, LOG1
log4perl.appender.LOG1 = Log::Log4perl::Appender::File 
log4perl.appender.LOG1.filename = /var/log/mylog.log 
log4perl.appender.LOG1.mode = append 
log4perl.appender.LOG1.layout = Log::Log4perl::Layout::PatternLayout 
log4perl.appender.LOG1.layout.ConversionPattern = %d %p %T - %m%n   

log4perl.logger.my_other_app = ERROR, LOG2
log4perl.appender.LOG2 = Log::Log4perl::Appender::File 
log4perl.appender.LOG2.filename = /var/log/mylog.log
log4perl.appender.LOG2.mode = append 
log4perl.appender.LOG2.layout = Log::Log4perl::Layout::PatternLayout 
log4perl.appender.LOG2.layout.ConversionPattern = %d %p %T - %m%n
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