[v5.3.0.2]
So I've had a lot of issues with coverage markers vanishing without knowing exactly why. Now I noticed Rider has a "Split Right" and "Split and Move Right", and I was using "Split Right".
When using Split Right you get a cloned tab without coverage markers. If you then close original tab, and the close new clone tab (without markers), it seems NCrunch will not show coverage markers for file again even if you reopen it, without having to restart IDE.
"Split and Move Right" however seems to work similar to vstudio's dito and makes NCrunch play more nicely.
*Edit: And.. even if you use the "..move right", if you navigate back in the left splitter Rider will re-open that file again in left pane (without markers) and you are back with issue having to restart the IDE...