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