C'est sans doute une question de choix de configurateur dans l'appel à avrdude :
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Option -D
Disable auto erase for flash. When the -U option with flash memory is speci-
fied, avrdude will perform a chip erase before starting any of the programming
operations, since it generally is a mistake to program the flash without per-
forming an erase first. This option disables that. Auto erase is not used for
ATxmega devices as these devices can use page erase before writing each page
so no explicit chip erase is required. Note however that any page not affected
by the current operation will retain its previous contents.