Isaac96:
The Arduino IDE is not designed for .hex files. Could you explain how you got the IDE to open the hex file from the barebone atmega328?
1 Open Arduino App
2 Write some code.
3 Compile code as you choose arduino nano board (They use Atmega328p) 
It will want to save it somewhere
4 When you ok, you go to Sketch > Export Compiled Binary , and in this momement , Arduino App make .Hex from you Project (.ino) and give you ( 2 things ).
Your project is blink , you will have a folder (blink) inside you will have 1 file named Blink.ino
2 one is named "Blink.ino.eightanaloginputs"
3 one is "Blink.ino.with_bootloader.eightanaloginputs"
then i Use mu USBavr clone with Averdudess 2.4 and burn it to the barebone atmega328 that have 16mhz cristal , 10kOhm to reset and 5 volts and work , you will have to see the coresponding pins of the atmega328 and bam its working no problem . Conection are Miso to Miso , Mosi to Mosi , SCK to SCK, 5v to 5V , ground to graund, RXD to RXD and TXD to TXD , Averdude recognize the Atmega328 and you choose the arduino nano priset . they you are done. The Bare bone arduino is working. Now You can download back the hex file in Intel Hex and you get the program from the atmega328 on the barebone. you can open it with the Arduino App , no problem just like the original files 2 , 3 that App give you . and you can reuploade and still works , no problem . The Averdudess have option to download from Arduino Nano board that is Atmega328 with 5v regulator and cristal for the clock . and USB to Serial Convertor IC. You program the arduino with the Arduino App directly and working like a charm . My problem start when for example i want to download the code from my nano that is working for severl years and i lost the original file . I go to Averdude choose arduino nano , Averdudess recognize the Atmega328 from the arduino nano (clone) original I Read Hex file just like the Barebone i made and have the hex file like the barebone , but when i try to open it the Arduino App give me Error , The Funny Part is How so Arduino App can export .hex and burn to a barebone atmega 328p and retreve it and i n the same time i cant read from arduino nano the same way 
I even try to copy the files and write in to them with no change of the format and still not working