MP3 is a compressed audio format. You can't just cut bits out and expect the remainder to still be a valid MP3 file. In fact, since it's a DCT-based transform, the bits are in the frequency domain instead of the time domain. There simply are no bits for sample 10465. There's a frame which contains sample 10465, and there's a set of bits describing all frequencies in that frame.
Plain cutting the audio at sample 10465 and continuing with some random other sample probably causes a discontinuity, which means the number of frequencies present in the resulting frame skyrockets. So that definitely means a full recode. The better way is to smooth the transition, but that's not a trivial operation. And the result is of course slightly different than the input, so it still means a recode.
I don't understand why you'd want to read 20 seconds of audio anyway. Where's that number coming from? You usually want to read everything.
Sound is a wave; it's entirely expected that it crosses zero. So being close to zero isn't special. For a 20 Hz wave (threshold of hearing), zero crossings happen 40 times per second, but each time you'll have multiple samples near zero. So you basically need multiple samples that are all close to zero, but on both sides. 5 6 7
isn't much for 16 bits sounds, but it might very well be part of a wave that will have a maximum at 10000. You really should check for at least 0.05 seconds to catch those 20 Hz sounds.
Since you detected silence in a 50 millisecond interval, you have a "position" that's approximately several hundred samples wide. With any bit of luck, there's a frame boundary in there. Cut there. Else it's time for reencoding.