I too had the same issue with the subwoofer cutting out frequently on my Sony HT-ST5000. The bass would suddenly drop out, and the green light on the front of the sub would flash slowly as if trying to reconnect. After 10 seconds or so the sub would reconnect and the bass would start playing. It started happening infrequently so was a slight annoyance, but more recently it started happening every minute or so, which was a big distraction. I also occasionally got a muddy thudding / flapping / fluttering sound from the sub, which sounded like it was blown. Turning it off and on again resolved the problem.
I tried all sorts of things to fix the problem. Moved the sub around the room. Plugged it into different outlets. Tried all combinations of the radio channels and frequencies. Enabled secure link. Replaced my WiFi router. Nothing I tried had any effect, which was frustrating.
I took out a 5 year warranty after reading some early reviews, and decided that it was better to get it covered for longer in case any any problems down the road. I dropped off the soundbar and sub at PC World for repair, which took a week. When it was returned to me, it seemed like the sub had a new plug on it, so I suspect they did so something to it. Anyway, as soon as I plugged it in the sub started cutting out again!! There was also some aesthetic damage to the soundbar and sub - a couple of nicks to the soundbar edge and it looks like the sub was dropped on one corner because the metal is scuffed and crushed. Grrr. I take good care of my things, so this is setting off my OCD a little! Might have to get back in touch with PC World / Currys and see what they have to say about it.
As a last gasp attempt to resolve the sub cutting out problem, I wrapped the power cord to the sub around a ferrite core a couple of times and this seems to have resolved the problem. I must have some RF interference on my home power supply which the sub is particularly sensitive to. So if anyone has had trouble with their sub cutting out or making strange sounds, then try putting a ferrite core around the power cable to see if it helps. You can also try a mains conditioner like a Tacima 6 way mains conditioner which you can get from Richer Sounds and Amazon.