On the origin site, I use export to generate a zip from multiple selected nodes. The zip contains the expected yml files and assets.
On the target site, I use the upload from zip option to import that zip file.
Any nodes from the origin that didn't already exist in the target appear to get created correctly.
But nodes that already existed in the target don't get touched. I've confirmed that the UUIDs and NIDs match. And it's the same result whether I've opted to require the site UUID to match or not.
It seems to have something to do with ContentImporter->importCustomValues() calling ContentImporter->setFieldValue(). If I track the state of the entity, if it's a node before that function runs, it stops being a node afterward. And indeed if I put a debug at the beginning of importCustomValues(), it is no longer a node after setFieldValue() is fired. So it's never saved.
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I think that this turns out to be another "me" problem. Our setup includes an odd custom entity that doesn't use UUIDs (you don't want to know the details), and that messes up the import.
It would be nice-ish if there were a graceful fallback for this kind of thing? But I'll have to take a look at that later.