Lightroom 6 Publisher

I’ve noticed that sometimes, a previously published site’s image thumbnails disappear from the Lightroom Publisher section but are still online. Also, when looking into Backlight/Publisher/…/ the images are there.
If I try to replace the thumbnails within Lightroom, then publish them, I get duplicate images on the web page. Trying to delete the files from Backlight gets the warning that this should be done in Lightroom! Can you see a reason for this?

Are the albums in question under Backlight or Lightroom control? You can check in a couple of ways:
In Backlight, look at the Albums page. One of the columns is named “Source.” This lists the source of the album: Lightroom or Publisher

You can also just edit an album and look under Advance Settings > Album Management

All my albums are published with Lightroom. This “disappearing act” has first been noticed a few years ago.
All I can do is remove the images from Backlight, the warning is ignored, and re-publish again via Lightroom.
As a matter of concistency, I like to catalog, edit and publish my images in Lightroom.