It should work. At least I see no reason, why it shouldn't. Just make sure not to do this:
fb.setBlittingShader(...);
fb.blit(...);
fb.setBlittingShader(null);
That doesn't work, because blits are buffered but the shader isn't. If you need to reset the shader in the process, make sure to execute the blits before. You can force this by blitting a dummy blit from some other texture. Like:
fb.setBlittingShader(...);
fb.blit(...);
fb.blit(...); // <- Dummy-blit (1x1 transparent pixel with some other texture or something)
fb.setBlittingShader(null);