First, I don't think it is necessarily a bad thing, if it is bringing extra layers of interpretation.
But I suppose you worry about completely losing the interpretation you want to push forward, or about creating plot holes.
I worry about that to. Although I have a precise outline and all important scenes already written for my long form comic, I tend to change, add, or remove content as I go.
The way I deal with keeping things consistent is re-reading all my comic until the part I'm changing, keeping in mind what I'm changing while I reread.
To make the reread more efficient, I first verify (or guess) what my change can impact. Will it impact the timeline, or one (or more) character, or the environment etc?
Then as I read I make a mindmap with all the info that will be pertinent to the part with changes. I make sure it flows logically.
Then I read the later developments of my story (after the altered part) and continue the mindmap to detect any inconsistencies.
I find that part is the most important: it's rare for me to write something inconsistent with what is already finished, but if I forget to alter the events AFTER the changes, I may mess up, because I can forget that I made any changes and assume my detailed outline is 'safe'.