The documentation at https://www.gpsoft.com.au/help/opus12/index.html#!Documents/Creating_Folders.htm is not entirely correct when it says 'If this is turned on the name field changes to a multi-line text box that lets you enter as many names as you like (one per line).' There seems to be a character limit on the text field. I have a long list of folders (~3000) that I pasted into the text field but it truncated at a certain point and would not allow additional characters to be entered. The character limit seems to be 29,244.
The default limit on edit controls in Windows is 32,767 characters (including the CR LF characters at the end of each line), so you're probably hitting that.
We may be able to increase it, but for the time being you would need to split the list up.
In the next beta, the limit will be increased from 32 KB to 512 MB.
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now that's a jump