Seems I was right (well, let’s see shall we…) in my hypothesis regarding swcs in the same folder as the fla. In order to test this, I started up a new Actionscript project in FlexBuilder and created an assets folder. In Flash I opened a new fla, which I saved into the folder and then began to load it up with assets. At 32.4MB and 130 odd symbols (including videos, vector symbols, images and sounds) my swc finally broke and wouldn’t import into Flex properly. I then created a swc folder in Flex Builder and set the fla to import into that folder. Importantly, I also deleted the swc + swf from the assets folder. After recompiling the fla and rebuilding my Flex project, everything magically worked again.
I hope this helps someone out!