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I dont want to disturb the file2,changes should be done at the same place as they appear in file2.

The modified # lines should not be appended at the end .

Targetfile:
IP = 127.0.0;...

reffile:
IP = 10.10.10.102;
#HostNameSelection = 0 ;
#DomainName = abc.com;#url1
Targetfile:
IP = 127.0.0;
#HostNameSelection = 1 ;
#DomainName = xyz.com;#url2

Targetfile should be...

this will give me the difference in the values of lines beginning with # , how to copy the value at same line?

I Have file1 with below lines :

#HostNameSelection=0 :NotUsed
#HostNameSelection=1 :Automatic
#HostNameSelection=3 :NotForced

I have file2 which has similar lines but with different values ...