Here's most likely what happened.
Before you had finished setting up your rosters in the prior week, you had already moved ahead to the next week. When the program moves forward to a new week, it checks whether you've been to that week before. If you haven't, it copies the rosters over based on the lineup rules.
So later, when you went back to prior week and made changes, and then moved forward again, the program remembered you had already been to that week before. Because of that, it kept that week the way it was the very first time you visited it — it did not update it with your new changes.
One thing to note: the program does try to warn you about this. When you move to the next week and there are no scores entered yet, it will show you a warning message.
Here's how to fix it:
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