So I must be missing something in preserving custom DLC worldspace content when removing a non-critical ESM dependency.

I have a mod that adds objects to the DLC worldspaces (Solstheim & Dayspring Canyon). It has masters of DB, DG and CoT. All custom objects render and behave correctly. Good version of the mod.

Next I make the mod independent of CoT by removing property/script references and the COT dependency. Nothing else is touched, including the custom DLC worldspace content. But when the mod is next loaded into the CK, the DLC worldspaces have duplicated themselves and my custom content is gone (assumedly in the duplicated cells).

Why would this happen? A user reported that Wrye Bash spat out an error that said the dependencies were out of order (easy to fix in TES5EDIT). Could this be a clue?

It depends on how you removed COT from your plugin.

Removed CoT property reference, saved esp, removed script references, saved, removed master dependency from data window (select esm ctrl+del).

Go one step back (if you have backups) and try "Clean masters" in TES5Edit instead. It should remove masters that are not referenced in plugin. If not, then there are still some references or overrides somewhere that need to be removed first.