> I am new to ffmpeg/avlib and what I am trying to do is just decode and encode 
> back again an aac file. I don't try to make any changes to the file although 
> the avlib encoder is producing a file with more initial padding than expected 
> and it is cropping the final frames of the audio clip.
> I exported the avframes created by the decoder and all the file information 
> is there. It is at the encoding step that I am doing something wrong.

It sounds like you are not flushing the libfdk-aac encoder at the end.  The 
encoder holds on to audio samples internally while you are encoding and you 
need to flush those last samples
When you are finished encoding.
- David
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