My canonical tag disappeared from the page source

Look at the line just above it. The usual cause is an unclosed attribute. If the meta description is missing its closing quote and angle bracket, like:

<meta name="description" content="My page description

then the browser keeps reading everything that follows, including your canonical line, as part of that content value, until it finds the next quote. The canonical tag is still in the file, but it's swallowed inside another tag's attribute.

That was it: the description line was missing its closing "> so the canonical was inside it. Thanks.

Quick ways to catch these: view the page in your browser's element inspector rather than the raw source, since the inspector shows how the browser actually parsed it. Or run the page through an HTML validator. Our Meta Tag Analyzer lists the tags the page really ends up with, so a missing canonical shows up straight away.