Compare plugin in Notepad++ allows you only to compare and see which lines are duplicated, it won't let you remove the lines that are duplicated.
You gotta do it yourself manually, and when working on files with 200k lines it's not the way to go.
i am not sure what you actually want to do, so i can not help you much
i can also suggest you to combine files and remove dublicates on the combined file, but this is probably not what you want
what i guess you actually want is to extract the entries in file 2 which are not in file 1
you can do this in the command line with this code
$ awk 'FNR==NR {a[$0]++; next} !a[$0]' file1 file2
as you can see , the code has $ in front so that means it should be bash
now to explain you what is written above
FNR is the current file's record number
NR is the current overall record number from all input files
FNR==NR is true only when we are reading file1
$0 is the current line of text
a[$0] is a hash with the key set to the current line of text
a[$0]++ tracks that we've seen the current line of text
!a[$0] is true only when we have not seen the line text
Now you can do this with another way aswell which is easier to comprehend
sort file1 > file1.sorted
sort file2 > file2.sorted
comm -1 -3 file1.sorted file2.sorted
This will output duplicates, so if there is 1 3 in file1, but 2 in file2, this will still output 1 3. If this is not what you want, pipe the output from sort through uniq before writing it to a file:
sort file1 | uniq > file1.sorted
sort file2 | uniq > file2.sorted
comm -1 -3 file1.sorted file2.sorted