It won't be an issue if you don't image your cRIO without the solenoid module in place.
Also, I don't think it will be an issue as long as you don't OPEN a solenoid. The issue appears to be if you OPEN an input or output, and either the input/output hardware doesn't exist, OR you double allocate something.
Will the imaging tool allow you to image the cRIO without the module in place? if so, that might be what happened.