Hello @kv2, Good Day!
Please share a picture of the communication frame in which the configuration of the oscilloscope or logic analyzer allows to interpret the commands sent and the response can be appreciated. Something similar to this but for the UART interface:

When you say that the interrupts are not being cleared, do you only refer to the IRQ pin not going LOW? Or did you observe the interrupt requests of the IRQ0 and IRQ1 register of the CLRC663 not being cleared? If so, how were they configured? And how did you test this?
Did you only modify what is shown in the patch file? Did you make any other modifications to register configurations or the initialization of the reader?
I would like to ask, how are you testing the example? Have you put an NFC tag close to the antenna of the reader and observed what happened after?
When using the SPI interface previously did you get the expected log?

Are you able to observe this log when using the UART interface?
Please consider that support in this specific scenario is very limited, since custom hardware is being used along with a third-party device. The related resource we offer is the NFC Reader Library for Linux Application Note, however, it is only for demonstrating purposes and any other implementation is up to the customer.
My best regards,
Daniel