Strange, I replied to this but the reply has gone. I only deleted the contents of the Picture Cache and Sonar didn't refuse to redraw them all, only some.
I managed to fix the glitching audio, I had a plug I believe was misbehaving and I Consolidated Audio so I'm not sure which was the cause, probably the plug.
I still haven't fixed the redrawing of the clips issue. I'm going to try deleting them again to see if getting prompted again fixes it. The data is good, it plays just fine.