The Hurd sources have stabilized again after a short period in which some of the interfaces were changed to prepare support of long files. All relevant filesystem and I/O interfaces have been modified to use 64 bit even on 32 bit systems.
In light of the small and patient user base, we decided to drop backwards compatibility and replace the interfaces instead extending them. This means that the binaries of the Hurd, the C library, and some other programs need to be replaced manually, all at the same time, followed by a reboot.
A detailed step-by-step procedure how to upgrade Debian GNU/Hurd is available on the Debian web site.
People not using a binary distribution need to do a full manual bootstrap. It is recommended to treat this as a cross-compilation case.