Unfortunately the RadUpload control does not support the scenario where you are starting the UploadSession and while the upload is still not complete to add more items for upload. The PrepareSelectedFilesForUpload method resets the collection of the RadUpload control.
The approach which you used in the code snippet below can be used to upload items programmatic-ally but once the upload session is finished. You could store the secondary selected items from the user and store them in a collection in your code-behind and once the Upload control finishes the upload of the items to programmatic-ally upload the secondary selected items.
I hope this information helps.
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