SLI bridge is needed for the GPU's to work in SLI. If you leave your computer off and remove the SLI bridge, re-paint it and reinstall it, and turn the system back on you will not need to re-enable SLI. However if you unplug the bridge and turn on your computer before re-installing the bridge you will have to re-enable SLI.
I would advise against removing the SLI bridge when the computer is on.
And I would recommend you use some masking tape to cover the copper connectors of the SLI bridge when you paint it, to prevent spray paint from getting inside and blocking the contacts.