Can patch files be changed after they've been created? If we remove these files, I think we should also remove the related changes from the patch files, see:
https://github.com/godotengine/godot/blob/master/thirdparty/sdl/patches/0001-remove-unnecessary-subsystems.patch#L360-L822

SDL update script should also probably be changed: https://github.com/godotengine/godot/blob/master/thirdparty/sdl/update-sdl.sh#L50

@bruvzg I can build and joystick works without either of these files, so I've just removed them. I also removed two other files related to IME which don't appear to do anything.

I do get a bug when compiling with threads=no which causes input to not work (can't click anything on the project selection screen) and

WARNING: Keeping screen on not supported by this display server.
     at: screen_set_keep_on (servers/display_server.cpp:579)

to be printed to the console, but my assumption is that this doesn't have anything to do with this pr.

Can patch files be changed after they've been created? If we remove these files, I think we should also remove the related changes from the patch files, see: https://github.com/godotengine/godot/blob/master/thirdparty/sdl/patches/0001-remove-unnecessary-subsystems.patch#L360-L822

Yes, the way I typically do it is to reverse the patch (e.g. with patch -p3 -R < old_patch.patch), stage changes, then reapply the patch, do the changes which are needed, and git diff > new_patch.patch. Then stage everything and commit. The new patch name can be the same as the old so there's just a diff on the diff :P

@Nintorch I removed the files from the patch which are no longer being compiled.

I'm not sure what to change about the update script, should I just rm the unused files?

Yeah you should rm the files (and their headers, also unused) and likewise delete them from the Godot repo.

diff --git a/thirdparty/sdl/update-sdl.sh b/thirdparty/sdl/update-sdl.sh
index 11a9d37f48..7aa8c2b915 100755
--- a/thirdparty/sdl/update-sdl.sh
+++ b/thirdparty/sdl/update-sdl.sh
@@ -49,6 +49,7 @@ cp -v io/SDL_iostream*.{c,h} $target/io
 mkdir $target/core
 cp -rv core/{linux,unix,windows} $target/core
 rm -f $target/core/windows/version.rc
+rm -f $target/core/linux/SDL_{fcitx,ibus,ime,system_theme}.*
 
 mkdir $target/haptic
 cp -rv haptic/{*.{c,h},darwin,linux,windows} $target/haptic

Thanks!

Cherry-picked for 4.5.1.