Recent I downloaded a lot of gedcom files from a repository.
Now I am deduplicating my trees. I have some questions
Child 01 has parents 11 and 12 = family 1112
Child 02 has parents 21 and 22 = family 2122
These persons are duplicates (01=02; 11=21 and 12=22).
webtrees reports possible duplicates 01 and 02, that's ok.
but webtrees doesn't report possible duplicates family 1112 and 2122, so before the final deduplicating I have to make a notice of the duplicate of 1112 and 2122, and merge these records manually.
... in similar cases when deduplicating, I'm doing it the same way you do. I notice all the additional necessary merge operations on a sheet of paper and do them manually. You are right it would be nice if webtrees would suggest these merges (new function); there are some other applications that offer after a merge operation additional merge operations for near relatives that are maybe duplicated, too.