I moved your topic to an appropriate forum category @adamabd12 .
In the future, please take some time to pick the forum category that best suits the subject of your topic. There is an "About the _____ category" topic at the top of each category that explains its purpose.
A firmware cannot hide a Com port. But the 32u4 has a native USB, so it can use another USB channel to communicate to the PC ( no USB serial Com port ). If you don't see a Com port in device manager, there is no serial communication.
That's not a 'hidden' comport - its the Com port to download a sketch to the 32u4. This port is always different to the Com port when communicating via Serial. This bootloader port is only open as long as the bootloader is running ( after reset ) and is used to upload firmware.
If there is no serial communication when the sketch is running, the IDE cannot reset the Arduino automatically for uploading. So you must do that manually when the IDE starts uploading the sketch.
One of the pins is the reset pin. You can connect that pin to Gnd via a button to get your reset-button.
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