What happens if you cover your eye for too long?

Depends on the cover. Keeping a normal healthy eye closed does not harm it, even for prolonged periods of time. If the eye is infected, it is usually better off not being covered, or else it could risk worsening of the infection.
Depends. What is too long? Why would you do this? Probably nothing. If covered to treat certain conditions, then it would be up to the treating physician. If there are issues, discuss with your eye care professional.