Follow-up Comment #8, bug #38659 (project avrdude):
As “programming” 0xff into flash is effectively a no-op,
what reason should exist to store these bytes in any file?
(Sure, in a binary file, intermediate 0xff bytes cannot be
omitted; in a hex or s-record file, even that would be
possible, but it's currently only done for trailing bytes.)
For EEPROM, things are different, because the assumption
is that EEPROM cells will always be erased on a per-cell
base right before programming. (Not all programmers and
programming methods actually [can] do this though.)
But for flash, the only way to revert it to 0xff is to chip
erase or page erase it (the latter only being supported by
programmers for Xmega devices, or by the SPM instruction).
Please discuss this outside of this bug report if you are
unhappy with it. It's not a bug but has been implemented
that way deliberately, so if there are fundamental objections,
this should be discussed separately on the mailinglist.
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