I found this post because I was also struggling with WinMerge. The line filter documentation goes right at RegEx, so did I. Stupid me; none of the expressions I made did any filtering. Turns out you just put the string in common to left and right lines and it works like I want.
For example, I am comparing 2 XML files for certain differences. Some lines contain these strings:
They are preceded by whitespace, and open tag string and followed by a UUID, which is the entity that is causing a difference I would like to ignore.
So I just added two line filters with just the strings and no RegEx stuff. It was a bit slow to process a 12M file, but I more than made up for the time in having to ignore 1000+ hits to see the 4 differences.
I think this is what you are after with the XXXXXXXX XXXXXXXXX on the left and right. I am assuming the data is the same on each side.