What exactly should I do here?  Skipping the eln support is not an option.

And the message is clear

 eln file inconsistent with current runtime configuration, please recompile:
 /home/apappas/.emacs.d/eln-cache/29.1-70b784e9/subr--trampoline-
 6b696c6c2d656d616373_kill_emacs_0.eln

simply remove /home/apappas/.emacs.d/eln-cache/29.1-70b784e9/subr--trampoline-
 6b696c6c2d656d616373_kill_emacs_0.eln

and restart.

(In reply to Antonios Konstantinos Pappas from comment #0)
> Issue: 
> A clean installation of spacemacs fails during initializaion with:
> eln file inconsistent with current runtime configuration, please recompile:
> /home/apappas/.emacs.d/eln-cache/29.1-70b784e9/subr--trampoline-
> 6b696c6c2d656d616373_kill_emacs_0.eln
> 
> Spacemacs had been working problem free until my last zypper dup
> 
> Expected outcome:
> Spacemacs works without problems
> 
> Steps to reproduce:
> 1. Install/update to latest emacs (29.1.4)
> 2. Follow the spacemacs installation instructions  
> git clone https://github.com/syl20bnr/spacemacs ~/.emacs.d
> mv .emacs .emacs.bak
> mv .spacemacs .spacemacs.bak
> 3. Open emacs and choose any keybind mode
> 4. Open it again
> 
> 
> Last known working release:
> emacs 29.1.0
> 
> I build the rpms from revision 357 locally and installed them with
> everything working as expected
> https://build.opensuse.org/package/show/editors/emacs?rev=357 
> 
> I suspect that 
> - Provide eln native shared binaries for all emacs program binaries
> in the recent updates may be the culprit.

Not a bug

Deleting the cache does not resolve the issue. Unless using spacemacs and probably other distributions is not a supported use case, I would suggest this is a bug.

Created attachment 869998 [details]
Output of  emacs --debug-init

(In reply to Antonios Konstantinos Pappas from comment #3)
> Deleting the cache does not resolve the issue. Unless using spacemacs and
> probably other distributions is not a supported use case, I would suggest
> this is a bug.

You have run

   rm -rf /home/apappas/.emacs.d/eln-cache/*

have you ... or in emacs the command native-compile-prune-cache ?

(In reply to Antonios Konstantinos Pappas from comment #4)
> Created attachment 869998 [details]
> Output of  emacs --debug-init

First line of the log shows

  native-lisp-file-inconsistent

And what is

  /home/apappas/.emacs.d/init.el

for?

Who is maintainer of spacemacs?

Seems that I've to forece that at update time the latest emacs-eln package has to be installed with the latest eamcs-x11 and/or emacs-nox packages as otherwise the binaries do not find their precompiled eln files ... should be fixed with the SR#1116811

I don't think this is the solution as the problem persists even after I remove emacs and emacs-eln and install again. The output of zypper info emacs-eln is then 
...
Name           : emacs-eln
Version        : 29.1-4.2
...

However running emacs-x11 works just fine while emacs-wayland shows the same issue.

Created attachment 870079 [details]
Output of bash -x /usr/bin/emacs

Try out

  EMACS_TOOLKIT=gtk emacs

this should enforce gtk as GUI ... does this work?

Yes, but this just launches the X11 version. 

➜  ~ xlsclients
localhost  emacs

(In reply to Antonios Konstantinos Pappas from comment #11)
> Yes, but this just launches the X11 version. 
> 
> ➜  ~ xlsclients
> localhost  emacs

Forget xlsclient ... see e.g.

ll /proc/$(pidof emacs)/exe 
lrwxrwxrwx 1 root root 0 Oct 11 15:30 /proc/2464/exe -> /usr/bin/emacs-gtk

Can you please start Emacs without Spacemacs to test?

I suspect you should try to delete the eln-cache and try again.

Please retest and compare with

  https://build.opensuse.org/package/show/editors/emacs#comment-1836530

No answer yet  ... pelease reopen if you face this problem again even with cleaned eln-cache