@HeatherPikairos OK I think I know what is going on. The Transfer Files node would not copy the whole structure but would try to put all the single files into the same (top) traget folder - which will result in unwanted structures.
To solve this one would have to use absolute paths (otherwise the List/Files node would ‘recognize’ the workflows and not include them and their files it seems) to scan all files and folders and then replace the original (source) path part with the target path part …
… and tell the Transfer node to use the individual target location:
Not sure if this is somewhat over-engineered 
but it should work. You might have to refresh the KNIME Explorer once it ran.
kn_example_transfer_workflows.knar (118.9 KB)