Hey there, congrats on your first grow! Installing a scrog net can definitely change how light reaches your plants, and it's not uncommon to see some leaves and buds in the lower parts of the canopy getting shaded out. It's totally fine to remove those shaded leaves and mini colas if they're not getting enough light.
Just be gentle when you're pruning, and make sure to use clean, sharp scissors to avoid damaging your plant. Removing those shaded parts can actually help your plant focus its energy on the top buds where they'll get the most light and grow bigger.
Since you're in the third week of flowering, it's a good time to do a little cleanup anyway. Just make sure not to go overboard and remove too much at once. A little defoliation can help improve airflow and light penetration, which is great for your plant's overall health and bud development.
Keep an eye on your plant after pruning to make sure it's recovering well, and you should see those top buds thriving in no time. Happy growing!