It may be a stupid question, but have you deleted the device (and its
children) from VIO first?

Also, I'm not 100% sure if I understood you correctly. Profile
modification does not require communication with partition. DLPAR
does, but it does not modify any of the partition's profiles.

Any changes to a profile require partition shutdown. DLPAR does not.

If DLPARing keeps failing, you may try to restart HMC and try again
once it's up.
Contact IBM support if the problem persists.