It actually has a setting specifically to accommodate this. From their FAQ:
"f.lux was created by people who care a lot about accuracy in colors. We know you want to make sure your colors are perfect so there is an option to disable f.lux for 1 hour at a time (for example, while using Photoshop). This setting returns your screen to its normal settings. In the future we plan to allow automatic disabling of f.lux when you launch certain programs. f.lux is not designed for use during advanced color work, but it's fine for layout or HTML. Currently, we don't recommend running f.lux on calibrated systems running Windows, but we expect to have a solution for this soon."
"f.lux was created by people who care a lot about accuracy in colors. We know you want to make sure your colors are perfect so there is an option to disable f.lux for 1 hour at a time (for example, while using Photoshop). This setting returns your screen to its normal settings. In the future we plan to allow automatic disabling of f.lux when you launch certain programs. f.lux is not designed for use during advanced color work, but it's fine for layout or HTML. Currently, we don't recommend running f.lux on calibrated systems running Windows, but we expect to have a solution for this soon."