my desktop drive icons are gone
launcher icons gone
top tray gone

dmesg -w

shows JWM is segfaulting error 10
/root/.jwmrc error is something like can't write for 5000milliseconds ...

How can / should I reinstall build in JWM?
How can startx use fluxbox?
.xinitrc seems to be able to detect KDE and XFCE

They're not gone. They're just hiding. They are still in the READ-ONLY puppy_fossapup64_9.5.sfs file on your storage media which is copied into RAM on boot-up. What did you do --install/modify-- to frighten them? Whatever you did resides in your SaveFile/Folder WHICH takes precedence in your 'merged in RAM' file system. See, https://www.forum.puppylinux.com/viewtopic.php?t=5818 and https://www.forum.puppylinux.com/viewtopic.php?t=6526

I'd rebuild your SaveFile/Folder unless you really want fluxbox. Creating a functional KDE or XFCE fossapup64 is a PITA. IIRC, someone already posted an xfce version. Do you know how to boot 'pfix=ram'? Can you boot into some other OS to edit your boot-menu?

FFR1, whatever you did; don't do it again.
FFR2, see https://www.forum.puppylinux.com/viewto ... 183#p97183 for how to boot as PUPMODE 13. Under PUPMODE 13 you can test anything you do without making it permanent>writing to you SaveFile/Folder. Just restart-x and test things likely to have been broken. If something has, reboot without Saving.
FFR3. when all is working well, boot pfix=ram and duplicate your SaveFile/Folder storing the duplicate in a place where it won't be used. Add a pfix=RAM listing to your boot-menu making it easy to ditch a broken Save and replace it with one which works.

Have you tried to do a reboot to get back to normal?

yes I have rebooted many times
Did find the culprit, I think
Screen would briefly show the icons, then vanish to be replaced by HOME TRASH icons,
after say 20 seconds the screen would go blank _
no killing X no console, nothing.

The culprit was ME plus adding pcman-gtk, it added another layer on the desktop hiding default JWM
and something else caused screen blank. rogue puppy event.

I thought JWM would be saved in save layer not RO,
maybe the timezones timestamps got flipped, who knows.

Back to a clean save file

AUFS transparently handles this. It will always write to the RW layer and if there is none then it will fail as usual.