\setupnotation[footnote][way=bychapter]

\starttext

\startchapter[title=One]

Chapter\footnote{Note 1} with two\footnote{Note 2} footnotes.

\stopchapter

\startchapter[title=Two]

Chapter\footnote{Should be Note 1} with two additional\footnote{should be Note 2} footnotes.

\stopchapter

\stoptext
