У вас должна работать строка awk:
awk 'FNR==NR{if(NR%2)i=$0;else a[i]=$0;next;}{if($0 in a){print; print a[$0]}else print}' file2 file1
EDIT
здесь я не вижу дополнительных линий. смотри тест. (возможно, ваш пример данных формата не совпадает с вашими реальными данными.).
однако я показал путь, как это сделать. Вы можете изменить awk oneliner, чтобы он соответствовал вашему реальному формату данных.
kent$ cat f1
/data/weather/date=2011-12-18
/data/weather/tempMaxC=25
/data/weather/tempMaxF=76
/data/weather/tempMinC=14
/data/weather/tempMinF=56
/data/weather/windspeedMiles=15
/data/weather/windspeedKmph=24
/data/weather/winddirection=NE
/data/weather/winddir16Point=NE
/data/weather/winddirDegree=39
/data/weather/weatherCode=112
/data/weather/weatherIconUrl=http:/someurl
/data/weather/weatherDesc= Cloudy
/data/weather/precipMM=0.0
/data/weather
/data/weather/date=2011-12-19
/data/weather/tempMaxC=29
/data/weather/tempMaxF=84
/data/weather/tempMinC=17
/data/weather/tempMinF=63
/data/weather/windspeedMiles=13
/data/weather/windspeedKmph=21
/data/weather/winddirection=N
/data/weather/winddir16Point=N
/data/weather/winddirDegree=360
/data/weather/weatherCode=116
/data/weather/weatherIconUrl=http://someurl
/data/weather/weatherDesc=Partly Cloudy
/data/weather/precipMM=14.1
kent$ cat f2
/data/weather/weatherCode=111
/data/weather/weatherIconUrl=images/icon1.png
/data/weather/weatherCode=112
/data/weather/weatherIconUrl=images/icon2.png
/data/weather/weatherCode=113
/data/weather/weatherIconUrl=images/icon3.png
/data/weather/weatherCode=116
/data/weather/weatherIconUrl=images/icon16.png
kent$ awk 'FNR==NR{if(NR%2)i=$0;else a[i]=$0;next;}{if($0 in a){print; print a[$0]}else print}' f2 f1
/data/weather/date=2011-12-18
/data/weather/tempMaxC=25
/data/weather/tempMaxF=76
/data/weather/tempMinC=14
/data/weather/tempMinF=56
/data/weather/windspeedMiles=15
/data/weather/windspeedKmph=24
/data/weather/winddirection=NE
/data/weather/winddir16Point=NE
/data/weather/winddirDegree=39
/data/weather/weatherCode=112
/data/weather/weatherIconUrl=images/icon2.png
/data/weather/weatherIconUrl=http:/someurl
/data/weather/weatherDesc= Cloudy
/data/weather/precipMM=0.0
/data/weather
/data/weather/date=2011-12-19
/data/weather/tempMaxC=29
/data/weather/tempMaxF=84
/data/weather/tempMinC=17
/data/weather/tempMinF=63
/data/weather/windspeedMiles=13
/data/weather/windspeedKmph=21
/data/weather/winddirection=N
/data/weather/winddir16Point=N
/data/weather/winddirDegree=360
/data/weather/weatherCode=116
/data/weather/weatherIconUrl=images/icon16.png
/data/weather/weatherIconUrl=http://someurl
/data/weather/weatherDesc=Partly Cloudy
/data/weather/precipMM=14.1
EDIT2
без .... Sameurl ...
awk 'FNR==NR{if(NR%2)i=$0;else a[i]=$0;next;}{if($0 in a){print; print a[$0]}else if ($0!~/someurl/) print}' f2 f1