Is there any evidence whatsoever that dietary L-Lysine is helpful against atherosclerosis? Yes, but

It was not until 2014, until a group in Japan studied a kidney disease related calcification disorder of the arteries.  It wouldn't be scientific to conflate this discovery to any other etiologies or use this for a cross claim where there was no evidence, although it recommends that L-Lysine be studied in atherosclerosis arrived through various pathologies.  A novel MOA, not considered before is the suppression of iPTH.  Very profound.  Importantly, they do not claim it reverts pre-existing calcification, and that this is an open question.  

The General Electric Lysine-Sepharose column for Lipoprotein(a) purification relies on the lysine binding sites (LBS) of apo(a) to capture it before eluting it with stronger affinity lysine analogs.  The study was never done in rodents to see if lysine could dislodge Lp(a) deposits in atherosclerotic plaque.  There certainly was ample time and resources available to do so and it remains an open question.

Dietary l-Lysine Prevents Arterial Calcification in Adenine-Induced Uremic Rats