This question is related to this one on small knots, but the solution there does not help (though it is needed in order for the intersections to appear at all.
My problem is the following: I'm drawing a knot with two intersections quite close to each other (a few milimeter apart), and I'd like to flip the first crossing, but not the second one. When I try to do so, however, nothing happens. When trying to flip just the second crossing, both flip. I'm fairly sure that this is happening because they are close to each other, but I don't know how to remedy it... Any help would be much appreciated!
MWE:
\documentclass{standalone}
\usepackage{tikz}
\usetikzlibrary{knots}
\begin{document}
\begin{tikzpicture}
\begin{knot}[end tolerance=1pt,flip crossing=1]
\strand[red,thick] (0,0) ellipse (0.35cm and 0.1cm);
\strand[blue,thick] (0,-1) -- (0,1);
\end{knot}
\end{tikzpicture}
\begin{tikzpicture}
\begin{knot}[end tolerance=1pt,flip crossing=2]
\strand[red,thick] (0,0) ellipse (0.35cm and 0.1cm);
\strand[blue,thick] (0,-1) -- (0,1);
\end{knot}
\end{tikzpicture}
\end{document}


\tikzsetin your preamble. The sort of thing I was drawing can be seen in https://arxiv.org/pdf/1602.06450v1.pdf – Andrew Stacey Dec 04 '16 at 19:14