I wrote an abstraction layer to allow using hardware and software I2C at the same time:
https://github.com/pepaslabs/AnyWireIncluded in the repo is a copy of SoftwareWire, as well as a forked copy of HTU2xD_SHT2x_Si70xx which has been modified to support AnyWire, and a demo sketch which reads from two temperature sensors, one over hardware I2C and the other over software I2C.
Cheers!