Beyond-compare wont ignore line-breaks?

I'm afraid it is not possible: https://stackoverflow.com/questions/10092538/how-to-ignore-line-breaks

even if you're ignoring line breaks, it won't treat the non-ignored text on separate lines as being continuous across line breaks.

this is not possible

I got an email from the company itself :

Sorry, it isn't possible to ignore line breaks.

This means:

one two

and

one
two

will always show as differences.

Comparison across line breaks is on our wish list for a future version of Beyond Compare.

Best Regards, Chris Kennedy Scooter Software