Files as well as folders kept in the flow directory are mostly interpreted as beans have a peek here. Beanflows determines the bean status according to its location in the flow directory structure. Done beans are stored in the _Done folder, inactive beans in the _Inactive folder, etc. When you set the bean status in Beanflows, the program will transfer it to the right folder. If you transfer the bean to a different folder in the Finder, Beanflows will show the right status.
The files and directories which are shared by beans in the flow, Beanflows stores in the _Flow_Items directory.