When you hide a row or swimlane, you also hide all of the task bars or milestones inside that row/swimlane. 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 on the Advanced tab of the Project-View Properties menu (see screenshot). Simply uncheck the Unhide rows for flagged tasks/milestones option (which is checked by default) and hit OK. (In versions 5.3 and later, this checkbox is found in the Crop options dialog box, accessed from the bottom left corner of the Advanced tab.) 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.