I have this same issue too.
On 05/02/2021 I had an evening with no Hori split pad pro issues.
After updating to 12/02/2021 after waking from sleep/off one of the controllers no longer functions.
If I slide the non functioning controller out of the rail and back in again it works but then the controller that was working no longer functions.
Only solution thus far is to restart and never let the Switch sleep.
I do not appear to have this issue when the joy-cons are in use.
I note @ponyboy82 also had or has this issue - https://forum.xda-developers.com/t/rom-unofficial-switchroot-android-10.4229761/post-84530409
I decided to bluetooth pair my Pro controller to Android and found the left and right triggers were not working.
Assuming this was relative to some analogue digital shenanigans I went looking for answers.
Found a relatable reddit post - https://www.reddit.com/r/switchroot/comments/k7a2v9
Unsure if this would work and resolve the trigger issues with the Pro controller I proceeded to flash the zip file mentioned in this post.
It did not work.
However since applying that zip file my Hori controllers are no longer exhibiting the issue mentioned prior.
Every cloud eh!
Have tested using Stadia, Geforce Now, PS Play, Steam Link and Xbox Game Streaming (Cloud and Local).
All appears well again!