I have the same issue, but I’ll add info on my setup. I’m also using an RGB modded SNES (via YPbPr + the analog input on the OSSC). I’m running the OSSC output into an HDMI switch, and the switch’s output into a splitter. Basically the idea is just to have a bunch of game consoles into the switch, which can then play on my monitor + be captured with my capture card. I initially blamed the switch/splitter for some issues, but found something interesting..
With my SNES, in Line 3x.. I get no audio from my monitor (BenQ XL2720Z), but I do get audio from my capture card (Startech USB3HDCAP, recorded via AmarecTV), simultaneously. Therefore, it seems the SNES output is correctly being mixed into the HDMI, and everything in the signal chain (switch, splitter) isn’t stripping the audio, and it’s just some quirk of how the display is handling that specific type of output when in >Line 2x mode?
I tested some other modes through the same display. Passthrough doesn’t display at all, out of range. Line 2x plays video and audio. Line 3x plays video but no audio. Line 4x also plays video but no audio, and also desyncs. Line 5x has no display. Video-wise, the monitor seems to handle Line 3x the best, with even aspect ratios being seamless.
I’ll also note for completeness that other devices through the same setup, which output at standard 720p/1080p, have no audio issues.