"Ignore" means "disregard intentionally." (from dictionary) "Ignore" doesn't imply that a line starting with "Title" must exist.
But the sentence says "the line". This implies that the person who wrote the instructions thinks that you will know which line starts with "title", so the person who wrote the instructions thinks that there is a line starting with "title" on the page.
And you should ignore that line.
The writer could have written "Ignore any line starting with 'title'". In that case there could be zero or more such lines.
The instructions don't say what to do if there is no line starting with "title", they just tacitly assume that one exists.
My interpretation would be that you should also ignore the absence of a line starting with "Title". I'd assume that the instruction means "Don't use the number on a line starting with title, only use the number on a line starting with version." So a page that has no title, and a line "Version 3.19" goes on the left. A page that has a "Title 3.19" and a "Version 1.01" goes on the right.