This hasn’t been addressed in Cubase 13.0.20 either 
I sent an email to Steinberg, let’s hope somebody sees it.
On Nuendo 13 and still experiencing this issue. Insane how it’s not solved and Steinberg touts “As the most advanced audio post-production solution available”. I open Nuendo to remind myself why I do professional work in ProTools…
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try sending an email to steinbergussupport@yamaha.com explaining what’s going on, Steinberg is “reviewing” my case but I think the more people see that is a serious issue the better, it’s really frustrating and it makes me consider switching to Studio One instead.
First post on this forum - first to say thanks to Louis_R for creating this thread with such detailed analysis, secondly to add that I’ve been experiencing many similar problems to different degrees, to the point where i thought i was hearing things and even go so far as having my guitars and basses checked for out of phase pickups.
I’m afraid i don’t have much to add but i’d just like to clarify what undesirable effects Louis_R is describing to make sure we’re definitely experiencing the same problems, specifically here:
But, from now on upon playback, it will start to introduce a slow phasing. It’s completely random, you can have a very low bleed for several seconds (-180 dB)
When you describe a ‘low bleed’ - is this similar to a very short reverb effect? If so this is what i’m sometimes experiencing when using AudioWarp (in addition to the phasing effects and the disastrous clicks and pops as comped takes are switched over). In my case it absolutely sounds as though there is a deliberate slapback reverb applied to the track - which obviously is not the case.
Re; the clicks and pops - these persist through mixdown and if i do a bounce selection on a comped take - the clicks and pops are now baked in permanently. 
meaning i had to send all the damaged clips to Izotope RX to remove these (incredibly loud) clicks.
Last thing i’ll add is that, all these effects that are being described are worsened considerably in the context of comped takes. To the extent that, at this time, i’m forced to chose between workflows; i can either use AudioWarp on a performance, or i can comp multiple takes of that performance together - i can’t do both.
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i’m forced to chose between workflows; i can either use AudioWarp on a performance, or i can comp multiple takes of that performance together - i can’t do both.
Just as an aside to this - can i get people’s views on what the best-practice procedure would be in a case where i want to use audioWarp on comp’d performance takes? (I suspect i’ve been using the two processes destructively )
Initially, i would first comp the takes together for the best parts of each performance - then, in the lanes view, i’d go to use the warp tool on the comp/selected events in each lane - but this would throw up a warning every time i went to use the tool on different events on the same lane that i was editing a file that was in use somewhere else. So i stopped doing it like this…
So resorted to the far more time consuming approach of audioWarping every performance on every lane before using the comp tool.
(sidenote - i don’t have anything to compare at hand, but i have a feeling this method actually resulted in even worse phasing effects and clicks and pops as described in this thread)
In an ideal scenario - i would comp the performances first, then bounce down to a single event/lane - then apply audioWarping to the final comp - but this doesn’t work when there are overlapping parts of the performance can’t be comped together until the overlaps are resolved… by audioWarping 
So just to restate - i’m curious what opinions / experiences anyone might have in order to mitigate these undesired effects when using these tools together.