I've encountered the same problem, in the Eastern Plaguelands.
It seems to only visually remove around 8 or 9 ADTs, until it stops working. The bugged ADTs are technically doodadless, but the doodads are still visible. I've tried starting from another location in the zone, and it always seems to occur after I shift the first few ADTs.
https://imgur.com/WnQyUW4
I've also tried blindly shifting all the remaining ADTs, and importing the doodads as gobs, to try to remove them that way, but the doodad is still visually there after I remove the gob.
'.phase shift doodads zone' works, but it also has a bug: with View Distance set to a high value, weird mountains appear in the distance, that are not really there, hence my wanting to shift ADTs one by one.
Weird mountains: https://imgur.com/RpCWZTe
Closer: https://imgur.com/avwAbCe
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