I did not see the real problem: the "chip erase" required before
programming resets the lock bits. That means that downloading (parallel
or serial programming actions) will practically always also erase the
bootloader (unless the EESAVE fuse bit is programmed, but so far I
looked for a solution that allows to download into flash and eeprom).
Atmel evidently expects that either the bootloader is used more or less
exclusively, or the programming mechanism - but not the kind of
combination I had considered.
Too bad. An alternative would be to use the calibration eeprom byte (I
use an external crystal) - but that is a kind of approach which
interferes with settings that are probably better left as they are
shipped with the part.
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