It appears that the New York State supplement to the MUTCD does not provide any information about whether a fluorescent red or orange flag may be used for traffic control. Can you clarify?
The National MUTCD states in section 6E.03 paragraph 09 the following:
“09 Flags, when used, shall be red or fluorescent orange/red in color, shall be a minimum of 24 inches square, and shall be securely fastened to a staff that is approximately 36 inches in length.”
Since this is not modified in the NYS Supplement it also applies to New York. Paragraph 11 of the same section indicates that a reflectorized RED flag should be used at night. The use of these flags should be limited to emergency situations only.
Remember, the MUTCD in New York State consist of both the National MUTCD and the NYS Supplement. You should first check the National MUTCD and then see if the NYS Supplement makes a modification. (http://www.clrp.cornell.edu/assistance/mutcd-info.html).
MUTCD 2009 Chapter 6E Flagger Control