UPDATE V2: Added batch generation for multiple new serial numbers for easier use with N2 Elite. The original version is still available for those who prefer the old method.

This python 3 script decrypts an Amiibo BIN file using Amiitool, generates a random tag serial, creates a new BIN file with the new serial, and encrypts it for use. Currently only set up for Windows but could easily be edited for use on Linux.
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AnalogMan is back with another cool scene release, this one is basically is designed only for those that use Amiibo emulating devices such as N2^Elite (aka) Amiiqo, Datel PowerTag or NaMiio. This app is no way designed for those who write Amiibo figurines to blank NFC tags or those with real Amiibo characters.

PLEASE NOTE: You will need to supply your own key_retail.bin file as the keys are Nintendo copyright. If you don't have one already it's the same one used with tagmo and found in the most common places that Amiibo BIN files are shared.

NEWS SOURCE: Amiibo BIN Serial Changer (via) GBATemp