Mind the Gap!"
It's not just an admonition made by British Rail: it applies to top-bar hives, too.
I have (slightly painfully ...) learned that bees do not want to see gaps above them with sunlight shining through, however small. Work from one opening, and, as you advance that opening down the length of the box, press all of the remaining bars completely together behind you so that no gaps of light shine through. For example, if you are examining each bar, open one working-gap, then press the replaced bars fully against their neighbors so that, at all times, there is only one gap.
If you need to briefly leave another gap, slide a suitable piece of wood over it in the interim, blocking the light. It does not seem to matter nearly so much how large (within reason ...) one opening may be. Likewise, if you need to step away from the hive, slide a similar thin board across the opening until you return. (Bees will come and go in the small space below this board, but this should be of no consequence.)
Bees become much more defensive of their hive when, obviously (from their point of view) the structural integrity of the entire hive is being compromised, and seeing several holes in the roof appears to be one such sign. That obviously is just cause for "General Quarters!!" ... as I am sure you would agree if you were a quarter-inch tall. However, when there's only one opening, be it large or small, well, bees are curious creatures.
If they do become more agitated, look for these gaps and close them ... running a bee-brush through them to avoid crushing anyone. When the number of gaps is reduced to one, the bees should calm down quickly. (Obviously, unusual aggressiveness should be taken as a possible sign of trouble.)
I have noticed this apparent correlation often enough that I wanted to bring it up.