Some people want to shoot either right or left handed, regardless of their eye dominance, and there is some question about whether it really makes much difference if you are shooting instinctively. But most instructors and texts recommend shooting with your dominant eye over the arrow. I mean, if you're shooting instinctively, you want the arrow to go where you're looking, and it's more likely to do that if the arrow is under your dominant eye. My experience is that if you switch sides, you will not feel uncomfortable with it after a week or so. It would be a good idea to start with a bow that you can draw and hold without straining.
However, none of this has anything to do with why you're shooting much worse than you were before. A little worse would be expected after a long layoff, but much worse means you're using bad form in some aspect of your shot without knowing it. Maybe if you switch sides, you won't repeat the form error. However, I can almost guarantee you that you will pick up others, because that's just how this game is played. Mastering the game means learning to identify your form errors so you can recognize them when they happen in the future.