There are 2 ways a zip can be opened:
- as a file, meaning a determined amount of data, which you can access randomly;
- as a stream, meaning a flow of data which you can read only sequentially.
SH3D uses the latter (ZipInputStream is mentioned in the stacktrace). It is well(?) know that this way of opening zip files may cause problems... I won't report the details here, but you if you are interested you can learn more here: https://commons.apache.org/proper/commons-compress/zip.html
So you may try rollback the libzip upgrade. This isn't a solution, but if we can identify the bug we can find a workaround and possibily fix it in the future. Please also post the version of the libzip you're using.