No, I hadn't made any changes to the existing pickup skills, I only added a new one. And then noticed the replay broke. After readjusting the pickup skill count to 4 and saving again, that's how things remained for the time being.
But anyways, thanks for clarifying that this is actually identical to cleansing, just the "manual" version of going about it!
That way, if this happens again, I can now rest assured I only need to manually correct it again once, and then it should remain in place after saving.
I had only reported this because I was fearing such a reset could potentially happen anytime I re-opened a level with pickup skill counts > 1. But since that doesn't seem to be the case, I think we can close this thread now.