Hi Ruby
Your question is very interesting. As FireflyTech says, there is a difference, but in the context that you are asking (battery compartment cover/lid), it is not easy to explain which to use.
Yes, in general, a cover could be considered larger than a lid, but not always. Also, lid is usually only used when it is a cover on the top of something. Also, a lid can only ever cover a hole in something while a cover can cover a hole and cover the whole object as well. To make things even more difficult, there are some occasions when only one or the other is correct. For instance, a teapot has a lid; a box has a lid; a dustbin has a lid; a drain can have a lid or a cover, but a manhole only has a cover!
I think that it is probably safer to use 'cover' unless you are certain that 'lid' is correct.