The only option is to put in addendum on the note, saying it was misfiled. This issue is common in all the major EMRs that I have used. I guess that allowing an administrative user to delete notes would compromise the medico-legal basis of the EMR. I agree that changing the location of a note isn't deleting it, but "digitally" it is still a deletion.
I am sure some type of deleting log would be a solution also.