Integration conflicts comparision beyond 20 thousand lines of code

Hi
SAP Netweaver , webdynpro for Java
I have a file which has 20 thousand lines of code in Project track and 16 thousand lines of code in maintanance track.
I have added 2 lines of code in maintainance track and tried to resolve integration conflicts with project track.
when i do Merge in integration conflict with project track.
it took so much time to compute difference and finally ended up with message
" Too many differences, Turn on the Ignore white space option or do a structure compare first"
once i click ok it takes to the comparison but its not able integrate as there are no signs of merging the code.
i am not able not find any solution for this to resolve this.
Could you please help me in this
regards
pradeep

Hi Satish and Anil,
Thanks for your reply.
Actually its only one activity that has to be integrated from Maintanance track( (4 new lines of code) out of 16 k lines) to project track which had 20 k lines of code.
Once i have released the activity from transport view of mainatance track it reached to consolidation tab of maintanance track and in parallel it reached to development tab in Project track(i have imported the same to consildation of project track) in CMS
After that i have gone to DTR and clicked on Integration conflicts the when i tried to right click and merge
it took so much time and finally ended up with message saying
" Too many differences, Turn on the Ignore white space option or do a structure compare first"
could you please help me this is critical for us to integrate the changes
Thanks and Regards
Pradeep

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