Like many other codecs AC3 hs fixed-length frames and encoder delay. One AC3 frame is 1536 samples long so at 48 kHz you have a frame-length of 32 ms. That will be the same with every AC3 encoder. Either work in WAV format incl. the append operation and encode after or at least try to find a better (e.g. silent) spot where you can append better.
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