I looked for this issue and could not find anything, sorry if this has been answered already.
The two pass method always worked for me with DynDOLOD versions 2.x
With 3.0 on the second pass with open cities active in the load order, i get an error:
Found Open Cities Skyrim.esp
Remove it temporarily from the load order
The only option is Exit DynDOLOD.
Per the manual, I did not alter anything in DynDOLOD_SSE.ini for open cities.
My DynDOLOD_SSE.ini contains:
;
; !!! NO NEED TO COMMENT OUT ANYTHING FOR OPEN CITIES !!!
;
; Parent world name
[Skyrim Tamriel]
IgnoreIfPluginExists=Open Cities Skyrim.esp
But it seems the plugin is not being ignored. I don't know what other information or files to attach here, but I will if needed.
Thanks for any help or advice