@grobasoz thanks for coming back to me. I am not sure I completely follow your post. What I did in my code was to essentially swap the columns for rows (from your original code) when going in and out of deep sleep since D6 (CPIO 43) is not a RTC pin (but all the row pins are). Logically I wouldn’t think that would make a difference to the logic/ability to go in and out of deep sleep.
I did use the RTC functions (rtc_io.h) as suggested rather than the GPIO functions (gpio.h) but didn’t make a difference.