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The "treat JPG separately" option has never immediately changed what the catalog contains, or shows.
If it did: say you have 100,000 Raw+JPGs loaded. And say clicking this ON caused LR to immediately create an additional 100,000 JPG entries in its Catalog, each one with its own preview, edit History, settings, collection membership etc. And more importantly, clicking this OFF caused LR to immediately delete all those 100,000 JPG images' previews, throwing away each one's independent edits and metadata and History in doing so. And any virtual copies made, too. that would be a really awkward and destructive scenario.
So what we have instead is the ability to just filter what images we see, operating from the images that ARE separately present in the Catalog; which requires the right importing to have happened.
The checkbox only changes what WILL happen hereafter, at import time (or, when you Synchronise Folder - which can be in effect, a means of import) .
If a folder contains a Raw+JPG pair and when that was first imported, the option was checked, an additional catalog entry will have been made at the time, to present the JPG independently of the Raw. If not, so such additional entry is there.
Changing the checkbox now, makes no difference to that prior import behaviour. But if you do some NEW importing, the behaviour for THAT changes hereafter.
So a new import operation (or Synchronise Folder) takes a fresh look at the actual folder contents, should disregard the Raw since that is already imported (good idea to tell LR to leave out suspected duplicates), sees those JPGs anew, and then does whatever the checkbox option tells it to, with those.
Note: doing this wholesale can put back any other photos present in the folder, Raw or JPG, which you had deliberately discarded from being imported to the LR Catalog.
Yep, Synchronize Folder is what I needed - thanks.
I've always had "treat jpeg files next to raw files as separate photos" checked so I think that setting got lost on an upgrade or somehow I must have accidentally cleared it.