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I have a sound recording roughly 40 minutes long at 24bit 96khz.
I've found that after trimming off about 40 seconds total of leading and trailing silence (well, quiet background hiss to be precise) from the original WAV and encoding to flac, the resulting file size is 40MB larger than the original recording encoded to flac!
Why would this happen?
Although FLAC encoding is always lossless, it still offers different compression levels to choose a tradeoff between size and decoding speed.
So, the unexpected difference in size that you noticed may come from different compression levels between the files.
Try to re-encode the cropped file with maximum compression level (8) and compare sizes again.
