I own a brand new 75 inch Q80t TV and a relativly new HW-Q80R soundbar. TV is on the brand new 1460.9 firmware and HW-Q80R is on 1012.6 firmware.
I have this problem with infrequent skipping sound when playing TrueHD/Atmos content from an external device connected to HDMI in the TV. This apply to both the PC connected to HDMI 2 and an Nvidia Shield TV Pro 2019 connected to HDMI 1. PC is set up to transmit Atmos sound for everything, so even Spotify skips when I play music from the PC, while the Nvidia Shield TV Pro skips when I play Atmos content from the apps on there.
I baught brand new high quality HDMI 2.1 cables to see if it fixed the problem, which it did not.
The audio skips happen roughly every 10-15 minutes. When it happens the sound skips for about 1-2 seconds, and the display on the soundbar shows the "Atmos by Dolby" scrolling text then "eARC" as the signal reactivates.
The skipping only happen with Atmos sound. Dolby Digital or Dolby Digital Plus works flawlessly.
Lip sync is perfectly aligned with all audio.
I am bumping this if you don't mind. I have a slightly different setup, but my issue seems related to your issue: https://eu.community.samsung.com/t5/audio-video/hw-q80r-shield-pro-2019-truehd-random-audio-pop/m-p/...
Something is going on with TrueHD/Atmos with the HW-Q80/90R, standalone or in combination with Nvidia Shield. My issue is 100% isolated to TrueHD/Atmos as well. Everything else plays fine.