“So you’re saying you export the SWF and play it immeiately in Flash Player and it’s fine? But once it’s imported to After Effects, all hell breaks loose?”
That’s the gist of it. I really have no idea how AE would alter a SWF after an arbitrary length of time, but it’s happening. I thought it might have to do with the cache so I purged it, but still nothing. I tried using the SWF (now edited by AE somehow) on another computer, and it was still altered.
This started happening after I got the mysterious “72×72” problem, where imported SWFs stop showing up completely in AE, and just appear as 72×72 blank icons in the browser. There was no way to reload or reimport the file – it would stay as a blank icon. As a workaround, I’d go back into Flash and export a new SWF and reimport it, which would fix the problem… until it would randomly happen again later.
The new problem of portions of SWFs vanishing is completely new, and it’s driving me nuts. Thanks for the read only suggestion – I’ll give it a go and see what happens. If nothing works, I’ll have to export the animations as PNGs and assemble them in AE, which is an extra step I’d rather not deal with.