Are all the multiple folders under one root folder or all over the place?
If they all live under one root folder you can do a search on that root folder for *, wait for it to list all file, select all, cut/copy and paste into a new single folder.
Found out that the cause was that for some stupid reason windows can't have more than ~22,000 files in a folder. Rather than informing me of this it gave me a cryptic error message, thanks for a well designed user friendly os Microsoft. (!)
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