Adding water mid-way through fermentation?

2 days ago I boiled a batch and transferred to a carboy for fermentation.

When I was pouring into the carboy, the wort was still a bit hot and my carboy (plastic) warped a bit at the bottom, so the inside volume is a bit lower than it should be. So basically after I added water to the wort I'm not sure if I have a full 5 gallons, I'm kind of having to eyeball it.
I was wondering if it would harm anything to add more water once I siphon into my secondary so that I can make sure I have exactly 5 gallons of liquid?

(I'll be using a glass carboy from here on out, also.)

Just let it ride.

When you switch to a glass primary, remember not to pour it in too hot. If the glass is too cool you'll break/crack the glass primary.

Don't add any water; being a bit off your volume is certainly nothing to worry about.

Volume is ok as long as your OG was close enough to what the recipe was estimating.

If it was hot enough to warp your plastic carboy, was it too hot to pitch the yeast? How hot was the wort after topping off?

You never need "exactly" 5 gallons. More than 5 gallons just means its weaker than the recipe. Less than 5 gallons just means its stronger (and usually better) than the recipe.
Sometimes I intentionally only make 4 or 4.5 gallons just to make a stronger beer.

I waited a while to let it cool before pitching the yeast. Everything else was done exactly to spec, only problem in this batch was that I deformed my carboy! OG was fine, just a tiny bit off what I was expecting.

I'll let it be though. Hell I like strong beer... Thanks for the help all!