ATMEGA32u4 RC variant programming issue

Hi all,

I have made a custom board using ATMEGA32u4 and everything works perfect. Recently, due to chip shortage and the availability of ATMEGA32u4-RC, I bought a few to put in my boards as a replacement. The problem is, after programming it for the first time, it doesn't program anymore.
it says the following:

avrdude: stk500v2_command(): command failed
avrdude: stk500v2_program_enable(): bad AVRISPmkII connection status: Unknown status 0x00
avrdude: initialization failed, rc=-1
Double check connections and try again, or use -F to override
this check.

Also, when I programmed it for the first time, it wasn't able to recognize the COM ports (which it always recognizes with a ATMEGA32u4).

Now, I have read the datasheet and know this type works with internal oscillator. But, I'm wondering, if there is a way to program them ? Any tricks /suggestions?
There's absolutely nothing on the internet.