Sounds to me like your pickup may be too close to the E string and is muffling it by magnetic interference with it vibrating. Try taking a measurement of the distance from string to pickup, then lowering the pickup on the E side by about the thicknedd of a dime or penny.
I don't know why this would have changed, but it's possible you have a loose screw on one end of the pickup and it has vibrated loose, allowing the pickup to move upwards.
It's also highly possible that I'm 200% wrong.
"The best way to tell a lie is to tell the right amount of the truth, and then shut up." Robert A. Heinlein