Hello fletch,
Yes I've seen this error. This error "vfiler has other references "means that your vfiler is being currently accessed at other places as well. Most common one is you have a vfiler context opened at some console and trying a cutover. This is not allowed.
Another but less common possibility is your vfiler is being accessed for by some ZAPI for some operation.
So close any vfiler context opened for that vfiler unit and re-try cutover. It will work.
warm regards,
Abhishek
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