Microblaze is a "soft" processor this means that the processor is sintetized in the FPGA logic like any piece of VHDL code.
Every time you re-program the FPGA you can change the feature of a "soft" microprocessor
i.e. one half of an FPGA can reconfigure the other half. So in your case, in one half you have a microblaze, and that can load some application dependant logic into the other, on demand.