Hi,
Regarding your issue that the ADC lost data when the USB is working, I suppose that the core is overloaded.
in order to reduce the core workload, I suggest you use ADC FIFO and set the watermark of FIFO to maximum, in the ISR, you read the number of ADC results in FIFO, then read them in one ISR, in this way, you can reduce the ADC ISR frequency and reduce the core workload.

Secondly, pls try to reduce the ADC triggering frequency so that the core workload can be reduced.
Hope it can help you
BR
XiangJun Rong