Follow-up Comment #2, bug #41928 (project avrdude):
How did you add support for the buspirate to the Arduino IDE? I don't think
it's supported out of the box. In Arduino version 1.5.x, the -D option is not
passed by default to external programmers defined in `programmers.txt`, so
it's likely that this is a problem in the way you added support for the
buspirate to the IDE (or perhaps a problem in the IDE, if you use version
1.0.x, which hardcodes more paths and options IIRC).
In any case, I think that running avrdude with -D and without -e is intended
to _not_ do an erase, meaning you can only change bits from 1 to 0, not vice
versa. If you're trying to flash in a new program, this is expected to
break...
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