I can not directly answer your question. However, I suggest following these steps:
With Classic, only SmartPreviews for the synchronized collections are uploaded and stored in the cloud.
If you deactivate synchronization for all collections, that should clear them from the cloud ... give LrC some time to sync.
To verify and to also clear the trash bin in the cloud, log in to https://lightroom.adobe.com and clear everything out that may still be there. Once all is cleared, deactivate syncing in LrC.
That should give you a clear start to move the images to Lr.
Please make to set up Lr correctly before starting to move photos, as by default every photo you import is stored to the cloud. If you want to work locally, make sure to verify the settings first.
Use the integrated migration option in Lr to move from LrC to Lr.
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