The word "operate" is essential to the meaning in this scientific-type text, so you cannot omit it. Furthermore, if you did omit it, the sentence would then be ungrammatical.
Please show us how you would rewrite the entire sentence, using 'reduce' instead of 'operate'. It will make make it easier for us to comment, and perhaps even for you to clarify your thoughts.
"Others contend that for a factor to be considered protective, in the presence of an existing risk factor, it must reduce the negative impact of the risk factor. "
Hi, "Others contend that for a factor to be considered protective, it must operate in the presence of an existing risk factor to reduce the negative impact of the risk factor.
"Others contend that for a factor to be considered protective, in the presence of an existing risk factor, it must reduce the negative impact of the risk factor. "
"Others contend that for a factor to be considered protective, in the presence of an existing risk factor, it must be able to reducethe negative impact of the risk factor. "
"Others contend that for a factor to be considered protective, in the presence of an existing risk factor, it must be able to reducethe negative impact of the risk factor. "
Do you think 'be able to reduce ' is the same as 'reduce'? I don't.