When you hide a row or swimlane, you also hide all of the tasks or milestones inside it. If, subsequently, the Flag value on one of those tasks gets changed in Project/Excel from No to Yes, OnePager by design unhides the row/swimlane so that the newly flagged task appears.
If this is not what you intend, you can easily suppress this unhiding behavior by going to Home > Project View Properties > Advanced and clicking on the Row Hiding Options button. This button was called Crop Options in earlier versions.
A set of row hiding options will pop up in a separate window. Uncheck the option to Unhide rows for flagged tasks/milestones:
From now on, hidden rows/swimlanes will always stay hidden, even if the Flag value on one of the tasks/milestones inside those hidden rows/swimlanes changes to Yes.