If you delete from collection, then yes, it will delete from both. You must select delete from playlist if you want it removed from just one folder (from left sided panel).
I agree that the scrolling down to my ‘playlist’ folder is a pain & I certainly preferred the old system of crates & playlists. I see 2.0 as a backward step IMHO but it is workable.
Tbh, the only benefit for me personally is the clock 
. Not bothered about the lighting & certainly not bothered about streaming. ZipDJ is awesome & regarding the reluctant acquisition of some ‘cheese’, I just buy individually.
Neither am I a fan of the new sync behaviour too. I also do not see the total number of tracks in each playlist (on the unit) & all in all, I generally see more bugs & less stability than any other version to date.
First & foremost, I think Denon should start fixing some long standing bugs (like channel leds increasing when actually turning down EQ knobs) rather than adding features. Best to fix some basics & to have top notch stability which brings greater confidence when playing out.