Your issues are not related.
Either you changed some other setting, you mistakenly unplugged the limit switch or some other mechanical problem was created. Your Z "0" position is off for some reason which made the printer think it needed to continue to go down. A picture would always be helpful in seeing exactly what happened, but if the divot is only 1 mm, I wouldn't even worry about it. Just shift your prints so they don't print in that area whenever possible. If it really bothers you, you can replace the bed plate on most printers.
Also, it's called a "print bed" or just plain "bed". I've never heard the term "hot base" before.