The problem with Fabric Softener is that is can build up on the fibres, so that the fibres can't absorb as effectively and therefore your nappies aren't as absorbent. I don't imagine a few washes would cause too much trouble, perhaps don't use as much detergent as usual (best not to use much anyway).

And just keep in mind, if your nappies don't seem as absorbent as they should be down the track, it might be worth a strip wash.