Issue creating cutting lines - Unchecking shapes to outlines produces opposite effect

[Vera3373295123rm]

I am trying to create correct cutting lines in my Illustrator file. The production company, who will produce the work and cut the lines, does not accept my file, due to 'double cutting lines'. The path is closed. I have tried using the 'flatten transparency tool' and uncheck the box for 'converting all strokes to outlines', but this seems to produce the opposite effect (the path is turned into a shape with a fill). This opposite behaviour only happens with pencil-drawn paths, and not with regular paths. Could this be the cause, and if so, how can I resolve this opposite effect?

[Monika Gause]

Just don't flatten or outline that path.

What kind of file do you save?