Answer

When exporting unknown documents you can face a problem that multi-page documents result in exporting each page as a separate document. 

The reason for this behavior is usually because import is set to automatic.
​
With automatic import, FlexiCapture splits documents into individual pages and when each page does not match a document definition, it saves each individual page as a separate document. 
​
In order to export unknown documents correctly, you need to set up your import as the following: 

This simple solution works stably with various unknown documents.