Follow-up Comment #1, bug #36901 (project avrdude):
Could you also try version 5.11.1? (You probably need to
select another Xmega device there, and override the signature
check with the -F option.)
I also recently noticed some Xmega PDI programming issues,
albeit for me they were only related to PDI through the
JTAGICEmkII, while the AVRISPmkII did work.
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