Yes, how I am doing it may be making my own life miserable, but it's the only way I know.
Details - as best I can give:
EXPORTING FROM: NR 4.0.9
IMPORTING TO: NR 3.0.2 and 4.0.9
I would import it, REPLACE the node, and do a bit of fixing up of other stuff.
ALSO: The subflow had been severely altered in that how many outputs there are/were.
Reduced.
Re-wire it and DEPLOY.
Things weren't working.
I'd inject messages and NOTHING happened.
After a few attempts, I would open the subflow and look at it's internals.
Half/all/most of the wires were missing.
Now, I'm not sure if I also re-exported it or just imported it again.
All wires intact.
WEIRD.
Just to put it out there.