UPDATE. Further experimentation has revealed the following, but still offered no viable solution.
It is not, as previously stated, that I can only open swf files saved to the desktop. It seems to be that I can only import files saved from one drive to another.
If a file is on one hard drive, and I export a swf to that same drive, the file fails to be read. If I export to another drive, any other drive, the file can be read. This seems to be the case in any combination, back or forth, so not limited to any one drive being the cause. It is the 'saved to same drive location' that is the constant fail.
Also, I installed a trial version of CS4 to see if newly created CS4 swf files can be read. They can. The error is limited to Animate and CS6.
This doesn't help me with work. It's too precarious.
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Adobe are you planning to look into this? We're having the same problem and it is completely halting our workflow.
Spiteyourface....we have solved our issue which was down to having a / in the file name. School boy error but as soon as we took this out it worked?
File formats changed when new versions of Flash Pro were released. With CS 5.5 there was a change to try to make files more future proof, and it's possible that a side effect stopped AE from using the files.
Now though there is a publish option for SWF Archive. If you open your FLA, go to Publish Settings, and check the box for SWF Archive, then Publish, you'll get a zip file that contains one swf per layer of the FLA. Those swfs should import into AE ok.