There's no mention about device model nor LE version that you are using and it may differ.
In general you need to change the Audio options in Kodi - Settings - System - Audio - Audio output device.
You also need to have the HDMI1 active (the device connected turned ON) when Kodi starts.
It works fine when configured properly (audio on HDMI1 while video on HDMI0) at least on RPi 4B running LE 9.80 Nightly builds ( Index of / ).
There are 2 things mixed, the bootloader itself and the bootloader configuration.
I believe you already have the bootloader you need (although maybe not the latest available) installed.
The firmware version check / update can be easily done from Kodi - Settings - Libreelec - Updates - Firmware Updates
So you can easily upgrade the bootloader and VIA USB firmware to versions contained in your LE package which are quite fresh.
A manual upgrade way is described here: RE: Is it possible already to set up a rpi4 with kernel 5.4?
There's also outlined how to show the bootloader configuration. If you wish to edit it, you must be at least able to connect to your RPi through SSH client (Putty recommended) and use nano editor. Both Putty and nano are easy to use. Default username is root, password libreelec.
After connecting to your LE, copy and paste these commands:
cd /tmp
vcgencmd bootloader_config > bootconf.txt
nano bootconf.txt # edit the current bootloader configuration as you wish, then press CTRL+X, Y, ENTER to save file
rpi-eeprom-config /tmp/pieeprom.bin --config /tmp/bootconf.txt --out /tmp/pieeprom
rpi-eeprom-update -d -f /tmp/pieeprom
reboot
You are not limited to SD card only, try USB 3.0 flash stick or SSD connected through USB 3.0 adapter.
Of course you can change the bootloader configuration, it's the same process in LE as in RPi OS (just without sudo as in LE you are root by default).
Raspberry Pi 4 bootloader configuration - Raspberry Pi Documentation
Also read here:
Yeah but it's strange that dead links are always much more easy found... 
Regarding to config.txt read here: Where is config.txt
Unfortunately the links to wiki are dead...
Do you get any response when you run the irw command and push MENU button on your RC?
Where do you run the command from?
Edit: Use SSH console to run the command and see the output.
In case you refuse all offered solutions, you should perhaps select another platform instead (RPi OS + Kodi)?
No problem. You may also look here for many other Video parameters for use in /flash/config.txt :
Video options in config.txt - Raspberry Pi Documentation
Perhaps you may try to force some HDMI mode which could possibly help to do what you need...
Yes it's always good to share...
No, I don't see any obvious issue.
The VL805 firmware release 000138a1 is the latest available.
Your bootloader dated 2020-09-03 is currently default/critical so it's also not bad but I would go to latest available and yet stable version 2020-12-11
You may see details here:
rpi-eeprom/release-notes.md at master · raspberrypi/rpi-eeprom · GitHub
The bootloader config looks also default, I am using a more complex/customized, like this:
[all]
BOOT_UART=0
WAKE_ON_GPIO=0
POWER_OFF_ON_HALT=1
DHCP_TIMEOUT=45000
DHCP_REQ_TIMEOUT=4000
TFTP_FILE_TIMEOUT=30000
ENABLE_SELF_UPDATE=1
DISABLE_HDMI=0
BOOT_ORDER=0xf41
USB_MSD_PWR_OFF_TIME=3000
USB_MD_LUN_TIMEOUT=5000
A detailed config params description:
Raspberry Pi 4 bootloader configuration - Raspberry Pi Documentation
Even with your current bootloader release, you should be able to directly boot LE 9.2.6 or LE 9.80 nightly from USB flash / disk, AFAIK all you need to do is to image it like it was your SD card (and maybe to add the preferred BOOT_ORDER parameter to bootloader config), connect to USB port, remove the microSD card and boot.
Then it was necessary to put this line to /flash/config.txt in LE:
dtparam=sd_poll_once=on
otherwise there was a repeating error message filling log due to missing SD card (not sure if it's still necessary).
Well, I don't see a big difference... Maybe a some timing issue?
As outlined earlier, I would try to:
double check the current mappings which should be exactly the same at the moment on both installations:
ir-keytable -r -s rc0
I would then run the irw command on LE 9.80 and press / release any RC button quickly to check online what happens - if you receive always the same number of commands (instead of just one) or if it is so sensitive to length of the push (and you receive for instance sometimes 3, sometimes 5 or even more commands in quick sequence).
You may also try to play with -D and -P parameters of ir-keytable to increase default autorepeat values.
-P, --period=PERIOD Sets the period to repeat a keystroke
-D, --delay=DELAY Sets the delay before repeating a keystroke
If nothing works, I would try to make a backup and install the latest fresh LE 9.80 Nightly from scratch.
It probably won't help but just FYI - it's possible to turn on / off HDMI outputs on RPi 4B:
HDMI display_power ON ALL HDMI ports:
vcgencmd display_power 1
HDMI display_power OFF ALL HDMI ports:
vcgencmd display_power 0
HDMI display_power ON HDMI port 0:
vcgencmd display_power 1 2
HDMI display_power OFF HDMI port 0:
vcgencmd display_power 0 2
HDMI display_power ON HDMI port 1:
vcgencmd display_power 1 7
HDMI display_power OFF HDMI port 1:
vcgencmd display_power 0 7
HDMI ports connection status:
cat /sys/class/drm/card0/*HDMI*/status
Also regarding to HDMI devices (re)detection just stopping / starting Kodi should be enough, it also take long time but it's still more quick than whole LE reboot.
systemctl stop kodi
systemctl start kodi
(or systemctl restart kodi)
At first I would check if the latest bootloader is installed (and upgrade it if not) - you can do it from Raspberry Pi OS as described for instance in this post:
RE: Is it possible already to set up a rpi4 with kernel 5.4?
Then look at / put here the bootloader config.
You may also try to install the nightly test build LE 9.80 or the stable LE 9.2.6 build to USB key instead of SD card.
Stop Kodi:
systemctl stop kodi
Start Kodi:
systemctl start kodi
No problem.
I am also running LE 9.80 (latest nightly from today) but on RPI4 and I am still still using the old custom mapping files (without .toml extension, which are still supported) and everything works fine.
As soon as you are receiving scan codes, you should be able to create your own mapping file (without .toml) in accordance with wiki and set the proper path to custom mapping file for nuvoton-cir driver in /storage/.config/rc_maps.cfg . After any change, you need to update configuration as outlined above (just with the path to /storage/.config/rc_maps.cfg instead of default /etc/rc_maps.cfg )
So the scancodes are received OK and there's a wrong mappings / different mapping file used.
rc_maps.cfg are equals
rc_keymaps folders in /usr/lib/udev/rc_keymaps , rc6_mce.toml and libreelec_multi.toml files are equals
Did you check the override folder (/storage/.config/rc_maps.cfg) as well or just a default folder (/etc/rc_maps.cfg) ???
I don't know the Milhouse's build but I thought LE 9.80 was the first build using .toml files...
If there're no overriding files and all the default config / mapping files are really the same, you may try to update the configuration:
systemctl stop kodi
systemctl stop eventlircd
ir-keytable -a /etc/rc_maps.cfg -s rc0 # for default folders
systemctl start eventlircd
systemctl start kodi
Then check the current mappings which should be also the same on both installations:
ir-keytable -r -s rc0
or run the irw command and push RC buttons to check online.
No, just tested if it worked.
I would like to use both HDMI outputs for video (a second display for webcams etc.), currently it's not possiblle but audio can be switched.
You can change the audio output in Kodi through Settings / System / Audio / Audio output device.
It's strange. Do you receive any scancodes when you try to run
ir-keytable -t -s rc0
and pushing keys on your remote control?
