waaaait... you have a CF card right?
do a backup to a CF card after you clear it out...
that would be the simplest...
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Well, I did some digging and there's some interesting aspects to this.
If I su 'zaurus' from konsole, I cannot seem to run qkonsole nor embeddedkonsole. It says permission denied even though it has execute permissions for all users. I also note that qpe.sh in /home/QtPalmtop seems to have set QPEUSER=root and QPEGROUP=root. I can also infer from the process table that the running qpe owner seems to be "root.root". Interesting behaviour to say the least.
I did try to modify qpe.sh which made my Zaurus not boot to desktop. I had to boot into commandline from startup and fix that up.
I don't have a CF card but I do have a 64 mb SD card. Kind of on the tiny end there.
I'm going to do a bit more digging but I find it interesting that in /etc/rc.d/rc5.d, there does not seem to be any link to running qpe...