Hello

This bug relates to Eglot and Flymake.  Demonstrating it requires a
language server program.  I don't think it matters which, but I will give
an example using python-mode and python-lsp-server (pylsp).

1. emacs -Q

2. Write the scratch buffer contents to a file with a python extension: C-x
C-w /tmp/test.py

3. M-x flymake-mode
Note the Flymake indicator in the mode line is
`Flymake:!`
indicating that all backends are disabled [1].

4. M-x eglot
Note the Flymake indicator in the mode line changed because the LSP is
providing Flymake diagnostic backends (I think they are pyflakes and
pycodestyle in the case of pylsp). The mode line looks like:
`Flymake[1 8]`
indicating 1 error and 8 warnings.

5. M-x eglot-shutdown
Note the Flymake indicator is now
`Flymake[0 0]`
indicating no errors and no warnings.

According to the manual [2]:
"Turning off Eglot means that it... restores the original values of the
Emacs variables that Eglot changed when it was turned on."
So the Flymake indicator should have returned to
`Flymake:!`

Thanks
Jake


[1]
www.gnu.org/software/emacs/manual/html_node/flymake/Mode-line-status.html
[2]
www.gnu.org/software/emacs/manual/html_node/eglot/Shutting-Down-LSP-Servers.html


In GNU Emacs 30.0.92 (build 1, x86_64-pc-linux-gnu, GTK+ Version
3.24.41, cairo version 1.18.0)
Windowing system distributor 'The X.Org Foundation', version 11.0.12101014
System Description: Guix System

Configured using:
 'configure
 CONFIG_SHELL=/gnu/store/6nqyia3ra10sgd1ppzk2047ncbzjwhff-bash-minimal-5.1.16/bin/bash
 SHELL=/gnu/store/6nqyia3ra10sgd1ppzk2047ncbzjwhff-bash-minimal-5.1.16/bin/bash
 --prefix=/gnu/store/c5805z2dvlmgay2hpwikvdlj2qciyclc-emacs-next-30.0.92-0.881d593
 --enable-fast-install --with-cairo --with-modules
 --with-native-compilation=aot --disable-build-details'

Configured features:
ACL CAIRO DBUS FREETYPE GIF GLIB GMP GNUTLS GPM GSETTINGS HARFBUZZ JPEG
LCMS2 LIBOTF LIBSELINUX LIBSYSTEMD LIBXML2 M17N_FLT MODULES NATIVE_COMP
NOTIFY INOTIFY PDUMPER PNG RSVG SECCOMP SOUND SQLITE3 THREADS TIFF
TOOLKIT_SCROLL_BARS TREE_SITTER X11 XDBE XIM XINPUT2 XPM GTK3 ZLIB

Important settings:
  value of $EMACSLOADPATH:
/home/jake/.guix-profile/share/emacs/site-lisp:/gnu/store/c5805z2dvlmgay2hpwikvdlj2qciyclc-emacs-next-30.0.92-0.881d593/share/emacs/30.0.92/lisp
  value of $LANG: en_AU.utf8
  locale-coding-system: utf-8-unix

Major mode: Python

Minor modes in effect:
  eglot--managed-mode: t
  flymake-mode: t
  tooltip-mode: t
  global-eldoc-mode: t
  eldoc-mode: t
  show-paren-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  tool-bar-mode: t
  menu-bar-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  font-lock-mode: t
  blink-cursor-mode: t
  minibuffer-regexp-mode: t
  line-number-mode: t
  transient-mark-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t

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Features:
(shadow sort mail-extr emacsbug message mailcap yank-media puny dired
dired-loaddefs rfc822 mml mml-sec epa derived epg rfc6068 epg-config
gnus-util mm-decode mm-bodies mm-encode mail-parse rfc2231 mailabbrev
gmm-utils mailheader sendmail rfc2047 rfc2045 ietf-drums mm-util
mail-prsvr mail-utils display-line-numbers time-date cl-extra eglot
external-completion jsonrpc xref diff diff-mode track-changes easy-mmode
ert pp ewoc debug backtrace help-mode find-func filenotify url-util
url-parse auth-source eieio eieio-core password-cache json map url-vars
imenu cl-macs flymake compile text-property-search warnings icons
thingatpt cl-seq python rx project byte-opt gv bytecomp byte-compile
compat compat-30 pcase treesit comint subr-x ansi-osc ring cl-loaddefs
cl-lib ansi-color rmc iso-transl tooltip cconv eldoc paren electric
uniquify ediff-hook vc-hooks lisp-float-type elisp-mode mwheel
term/x-win x-win term/common-win x-dnd touch-screen tool-bar dnd fontset
image regexp-opt fringe tabulated-list replace newcomment text-mode
lisp-mode prog-mode register page tab-bar menu-bar rfn-eshadow isearch
easymenu timer select scroll-bar mouse jit-lock font-lock syntax
font-core term/tty-colors frame minibuffer nadvice seq simple cl-generic
indonesian philippine cham georgian utf-8-lang misc-lang vietnamese
tibetan thai tai-viet lao korean japanese eucjp-ms cp51932 hebrew greek
romanian slovak czech european ethiopic indian cyrillic chinese
composite emoji-zwj charscript charprop case-table epa-hook
jka-cmpr-hook help abbrev obarray oclosure cl-preloaded button loaddefs
theme-loaddefs faces cus-face macroexp files window text-properties
overlay sha1 md5 base64 format env code-pages mule custom widget keymap
hashtable-print-readable backquote threads dbusbind inotify lcms2
dynamic-setting system-font-setting font-render-setting cairo gtk
x-toolkit xinput2 x multi-tty move-toolbar make-network-process
native-compile emacs)

Memory information:
((conses 16 132404 24100) (symbols 48 11396 0) (strings 32 34165 1733)
 (string-bytes 1 1222044) (vectors 16 24227)
 (vector-slots 8 666761 12385) (floats 8 58 44) (intervals 56 1035 0)
 (buffers 992 16))