I am confused regarding your post.
"The bilge" is an area of the boat, the lowest part, typically where water collects. The bilge can't "go out". The bilge pump, which removes unwanted water from the bilge can fail. The bilge blower, which provides ventilation and removes unwanted fumes can fail. Either of these can fail without any immediate risk to the engine but you should fix them as soon as possible.
When you said "we didn't realize it until we pulled it out", does that mean when you left the dock to go skiing, or when you pulled the boat out of the water to put it away? I normally do my boat maintenance with it sitting on the trailer so I don't see a problem here, unless "pulled it out" means that it was put in storage and you can't get to it anymore.
Any way you look at it, if the engine was running okay when you stopped using it last then it is probably okay. Fix whatever is wrong before you use it again.