After I import a .swf's into After effects the content disappears!

I have been using this work flow for sometime. I hand animate a sequence or a still of a character in Flash Pro on a single timeline, no scipts, etc just clean keayframe animation or a single frame.
Then export the sequence as a .swf.
Then usually import it into After Effects and use the vector output in my AE scene.
After completeing an animatic for a client last week all the swf's in my AE project are EMPTY. I tried re-exporting from flash and reimporting into AE and again they show up 1st time but if I close and reopen the project they are GONE again!!! Help I have been doing this same process since CS4 and I have master animations in AE files that I'm now scared to death to open because AE will make my work vanish...  

I'm having the same issue since updating to cs6. Have always used this workflow seamlessly until now. Some info:
CS6 Production Premium
All lastest updates installed - yes
Windows 7 home Premium
Processor: Intle core 2Duo CPU E*400
6BG RAM, 2 drives (AE running off ssd)
No external HD attached
Sometimes, but usually not running Flash and AE at the same time
No error messages
.swf's play fine in their own right outside of AE
No special filters, effects of third part plug ins operating
On save, some (not all) swf's lose some content. Its always the same content. Every time AE is closed and reopened the the same stuff is missing. Only fix so far (which becomes extremely annoying) is to rename the .fla and export a new .swf. It lasts until the next close/open.
As far as I can tell, it targets non-symbol assets moreso that symbol assets, but converting the problematic parts to symbols in Flash does not rectify the problem once it has presented itself.
Suggestions?
Amy

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