Yes it may be better to try smaller batches. You could create a new catalog:
File >> New Catalog
Choose a new catalog name and save by clicking Create
When the empty catalog opens try importing again.
You could start with the 2000 folder, perhaps when moving, choosing a new sub-folder e.g. 2000 New and then selecting dated folders. The destination panel should give you a preview of how many dated folders will be created and the number of files in each.
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