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Does my memory betrays me or once upon a time there was the checkbox "ignore line end (type)"?
(Not kidding, I really suspect I'm confusing with another program.)

I suppose it can be done using "ignore parts of each line matching regular expressions" but (I'm not very strong on regular expressions) I failed ignominously.

Can you please help me?

Options | Tex Compare | Ignore | Linebreak styles.

So such a checkbox exists!
I also was (almost) convinced I had it checked, and I was surprised when the linebreaks were not ignored.

Apparently I unchecked it for a test sometime ago then forgot to restore it.

Sorry for the stupid question.
I looked in the help for the wrong keyword. ("end of line" instead of "linebreaks")
Bed time...

Thank you.