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F/6 is fine. Cone isn't steep enough and even then you'd only miss the emission line bandpass ever so slightly. You sure its not present in any of your broadband data sets? SII or for that matter most narrowband filters require flats to be taken at considerably longer exposure times to reach the target ADU. I suspect you'll find that the issue will be corrected by flats. At least if its optical train configuration related anyway. Check there's no shiny edges of accessories in the optical path.
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