Yes. Wait, no.
OK, I know what you mean.
There is no real reason to remove it unless it is wood frame and rotted.
Just make a frame for the inside with insulation and cover it. Depending on
accessibility, you can do the same for the outside. If you leave it in,
some day if the window is needed, it will be there.
I have the same situation you do. My 2 basement windows are below a
deck. When I had new windows put in my house, I also changed those 2
windows. I'm glad I did. Even though I have 2 other basement windows
that are unobstructed, the 2 windows under the deck can still be
opened if I need to. Plus, what I plan to do in the future is put
lattice around my deck instead of 1X6 that are there now, so I can see
in my backyard from the basement window to look for the kids.
The replacement windows are cheap enough, probably easier than to block
the windows. Also you have a means of egress in case of an emergency.
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