That’s interesting… I have the same problem.
The remote was working on the previous version of CE (sorry I don’t remember the exact version) and after one manual update to 8.99.1.1 stop working.
More or less the same situation, no dtb.img at /flash, with one remote.cfg. Like @anthonws, I not made a clean install, was an update.
My current status:
CoreELEC:~ # ls -l /flash
total 147864
-rw-r--r-- 1 root root 40775 Feb 4 23:31 dtb.img
drwx------ 2 root root 16384 Dec 18 2016 lost+found
-rwxr-xr-x 1 root root 151355392 Jan 1 2015 SYSTEM
CoreELEC:~ # fdtget -t s /flash/dtb.img /meson-remote/ status
disabled
CoreELEC:~ # fdtget -t s /flash/dtb.img /meson-ir/ status
okay
CoreELEC:~ # ir-keytable
/sys/class/rc/: No such file or directory
No devices found
CoreELEC:~ # cat /proc/device-tree/le-dt-id
gxl_p212_1g
—UPDATE—
Fixed after copy the dtb.img to flash, remove the remote.conf from flash and force a Re-Update as described in this other post.