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