Mass-effect – Do you need a piercing mod equipped to shatter the Atlas Mech’s canopy

You can't carry Heavy Weapons around in this game. If you switch from them, you drop them.

When you pick up a Heavy Weapon, it temporarily replaces your current weapon from the weapon select wheel - the reason you couldn't find your Assault Rifle was because you technically still had it as your active weapon.

So you then switched to your pistol, which dropped the Heavy Weapon (on the ground nearby, able to be picked up again).

After this, your Assault Rifle should have been selectable again. Did you only try to switch to the assault rifle while you were carrying the Reaper Blackstar (the Heavy Weapon you found)?

Any projectiles which benefit from the piercing (in this case, penetrate a .5 meter thick object) will deal reduced damage (60%). Projectiles which don't need to penetrate cover or an obstacle to hit their target do normal damage. This includes the visual armor that Husks / Cannibals can get, and the shields of Cerberus Guardians.

Additionally, depending on the type of enemy and the difficulty, some enemies have "Armor" (not to be confused with the yellow Armor bar some enemies have on top of / instead of health). This armor reduces damage by a flat amount, and it is this Armor that the piercing mod works against. So you do get some benefit when attacking all colors of health bar.