Question If I send a digital signal via the TOS link input and then output the signal via the S/PDIF digital output, does the BMC-2 then re-clock that digital input Also, does the BMC-2 re-clock everything to 48 kHz

Yes. The signal would be re-clocked through precision JET PLL, bit transparent WRT data. Wrt re-clocking everything to 48 kHz: the BMC-2 is always 100% synchronous. It re-clocks the selected input regardless of its sample rate between 44.1 and 96 kHz.