Intra-line coordinates are cached, but cursorCoords always goes through the line height data in the document tree to get the line’s base height, which should be updated as soon as a line is redrawn. If I try to reproduce this in http://codemirror.net/demo/variableheight.html, I can’t—the coordinates at the start of the 3rd line change immediately when I remove the # on the first line.
Are you sure you’re testing this right? Can you set up a small demo that shows the issue?