There are only two reasons for losing position of the pedalboard.
1. Lack of pedal preparation.
2. Lack of focus.
As you might know pedal preparation is the secret technique that not too many organists use but it would help you to make your pedal playing very powerful and automatic. When you master your piece and apply pedal preparation, you never have to look to your feet in order to find the right pedals to play.
Pedal preparation is best practiced repeatedly with the short fragments of the pedal part in a very slow tempo. For example, repeat the passage of two measures 10 or more times while playing very slowly.
More importantly, as you release the note with your foot, with one swift motion slide it into position for the next one and let it rest there. Don‘t play the next pedal yet but let it wait for its turn. This of course applies for any of your feet, left or right.
Using pedal preparation doesn‘t guarantee the success, though. What you also need is to focus your mind. Focus is your mental attitude where you put you conscious mind into the current measure that you play.
No matter what kind of thoughts enter into your mind, don‘t fight them, don‘t think about them and don‘t worry about them. Simply be in the current measure. This is easier said than done of course but one thing which really helps to focus is your eyes. Fix your eyes on the measure that you‘re playing.
If you do this often enough, little by little your mind will learn to focus and you will have no trouble in finding the right notes and maintaining position on the pedalboard.