The easiest way to merge two files is to copy and paste. Notepad++ has no build-in file merging feature.
You can, however, install a plugin for this. See Combining files in Notepad++.
Another solution would be the command line's
copy. See Need to combine lots of files in a directory
Replacing line breaks:
Removing duplicates will be trickier than removing short words since Notepad++'s search does not search over multiple lines at once, so we will have to convert the line breaks into something else.
To achieve this, you can perform an Extended replace, finding all
\r\n (DOS line break) and replacing them by
# (or any other character that does not appear in your list).
If the last line was not blank, append a
# to the end of the resulting string.
Now perform a Regular expression replace, finding all
([^#]+)#(.*#)\1# and replacing them by
If there were duplicates in a single file, you might have to do that more than once.
Removing words of 4 or less characters:
This one is easy. Just perform a Regular expression replace, finding all
#.?.?.?.?# and replacing them by
Now you can get rid of the line break hack. Just perform an Extended replace, finding all
# and replacing them by
Finally, delete the last line as it will be blank.