If I've got your point - you need to convert single \r\n
to space but leave double, triple and so on.
You can use replace function of Notepad++ and this regular expression
(?<!\r\n)\r\n(?!\r\n)
Here we have negative lookbehind of \r\n
, then \r\n
itself and then negative lookahead of \r\n
, so it matches single occurence of \r\n
having no predecessors and no successors of the same characters.
Something like:

Note: you have to check "Regular expression" radiobutton at the bottom of form. Also field "replace with" should contain single space character.
As a result it converts following text:
line1
line2
line3
line4
line5
into this one:
line1 line2 line3
line4 line5