My understanding of what you are trying to achieve is to basically replace all the originals that you currently have stored in the cloud with smart previews synced up from LrC, while retaining the existing collections/albums in LrC/Lr. If that's correct, and you've already populated the new LrC catalog with the originals that are in the cloud, the next step is to delete the cloud originals while retaining the contents of your collections in LrC, yes?
To do this (you should test this on one collection first, but for the test make sure that you choose a collection whose images are not in any other collection), the first thing to do is to unsync the collection by clicking on the sync icon in front of the collection name. That does not do anything to the images in the collection, i.e. they remain synced, but it does stop them being removed from that collection when you stop the images from syncing.
So the next thing to do is select all the images in that collection, then click on the All Synced Photographs special collection in the Catalog Panel in LrC. That shows in the grid all the currently synced photos, with one of more of the selected images still showing. Without losing that selection, right-click on any one of the selected images, and select "Remove from All Synced Photographs". That will effectively delete those selected images from the Cloud.
Wait for that deletion to sync through to the cloud, easiest way is to open the Lightroom app (or the LrWeb online app in a browser) and wait for the All Photos number to reduce to match the new All Synced Photographs number. You will see that the Album that corresponds to the unsynced collection will also have disappeared, but the unsynced collection should still be there, as will all its images, though these will now have lost their individual synced icon.
When the change has fully synced through to Lightroom, go back to the collection in LrC and sync it again by clicking in the checkbox in front of the collection name. That will then cause LrC to upload smart previews to the cloud, the images will get their synced icon back, the corresponding album will appear back in Lightroom and will contain the smart previews.
The only thing you lose by this process will be any Folders that you had previously created in Lightroom, as they do not sync with their corresponding Collections Sets in LrC, so you'll have to recreate them yourself in Lightroom/LrWeb.
One other thing you should do before commencing this is to identify all the images not in any collection/album and to put them into a temporary one. Using Lightroom, first create a new album and give it a meaningful name, then click on All Photos, then click in the search bar. Select the Album facet and in the list that appears scroll to the bottom and select "Not in Any Album". That will populate the grid with all the synced images that aren't in any album/collection. So select all those images (Ctrl/Cmd+A) and then drag them and drop them into that newly created album. Back in Classic you will find the corresponding collection appearing in a "From Lightroom" collection set in the Collections Panel.
Once you are happy the procedure works you can do it all in one go, i.e. unsync all the synced collections in LrC (including the new one containing all the previous "not in any album" images), go to All Synced Photographs, select all and then right-click to remove all from the ASP. Wait until you are certain that the mass deletion from the cloud has finished (it may take a while, so don't get impatient), then when the cloud is empty you can then resync your collections which will upload all the smart previews and create the corresponding albums in the cloud. Suggest doing that gradually so that you can better monitor the sync upload progress.
Post back if you have any questions.
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