The underlying cause could be completely different in your case, but I had a similar problem running various arcade hardware (CPS2, CPS3, MVS) via a supergun with my OSSC. The frequency of sync drops was about the same: maybe once every 20 minutes on average, but it varied and sometimes I could play for 45 minutes with no issues but sometimes it would happen after 5 minutes. I don’t understand the reason, but I found that plugging my supergun into a different mains socket on the other side of the room dramatically reduced the number of sync drops. It hasn’t completely cured the problem, but I only see a sync drop maybe once every three or four hours on average now. Doing this also reduced some video issues I was having with the CPS3 (‘ghosting’ and some vertical banding at the left edge). It’s a long shot but I’d suggest trying the same thing just in case it helps.