I have the exact same problem.
TiVo is HDMI 1 on TV
Sound Bar is using ARC on HDMI 2 on TV
Roku Express is using HDMI 3 on TV
The audio drops while watching the Roku box. More frequently, the sound is absent when powering on the TV for the first time each day. No sound from the soundbar and no sound from the TV speakers (but only because ARC active on the TV settings). Once the sound drops, I am able to get sound from the TV speakers IF I change my TV settings back to "TV speakers only". Changing it back to ARC? Well, no sound again.
The quickest workaround for me is to unplug the Roku box for a few seconds, and plug it back in. When the Roku box is powered back on, it takes a few seconds for the TV and Soundbar to handshake, but the sound returns via ARC, regardless of the current input source.
Fact: Unplug the Roku box, and I NEVER have audio issues via ARC/Soundbar.
The Roku box interfere's with ARC. HDMI cables can be left in place.
I suspect a Roku update could fix this.
It's so ridiculous that I'm considering wiring an inline power switch for the roku.