I have seen this many times and I know we need to manually modify the boundary and stream networks in some cases.
However, i have never seen a publication specifically discusses this issue.
Serious answer only, please.
Dear Chang Liao,
I suggest you to see links and attached files on topic.
https://hal.archives-ouvertes.fr/hal-00925688/document
https://pubs.er.usgs.gov/publication/pp1604
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