Hello, long time Renoise user here.
I decided to write, because it’s probably the first time I noticed such annoying bug (feature?).
When using combo of:
The render comes out bad. It’s like, when the note is triggered, you can hear previous note right before it.
Try it for yourself 
test.xrns (5.0 KB)
Yeah that sounds messed up!
The NNA is set to CUT, yet when rendered there seems to be some some feedback from previous note.
Unfortunatly ive never really used the obfuscation feature ‘phrases’ so i’m not sure why tbh.
test2.xrns (1.2 MB)
With the phrase deleted and the hidden notes brought out into the main pattern; the render is good.
test3.xrns (1.2 MB)
Not sure if anyone has some way to fix this ‘Phrases’ issue or not; seems it may require development.
It’s a specific problem with the I/O commands in combination with phrase playback, so that needs a fix in Renoise.