Back in my days as a Unix C programmer, we used to use a tool called "diff". You could dump the output from diff to a file, and then use another tool called "patch" to merge the changes to another file. Does UltraCompare have this feature? I can't find it anywhere.
You can create a diff file with UltraCompare. But it is not possible with UltraCompare to apply this differences later to another file. You can write an UltraEdit script or macro to do that. But UltraCompare Professional supports 3 way file compares. With that feature you can compare 3 files at the same time and merge the differences between file 2 and 3 into file 1.
Best regards from an UC/UE/UES for Windows user from Austria
If you really need patch and not a three-way merge, you can get a version that runs on windows here:
http://gnuwin32.sourceforge.net/packages/patch.htm
http://gnuwin32.sourceforge.net/packages/patch.htm