from the examples given, my guess is that the need is for any sub-string matching  "__A_" or  "__A_A_" (where  A is any alpha character) to be replaced by  "__" (a double-underscore). (i assume the "g" in "__gPopalzi" is a typo.)

in that case, this may be appropriate (UNTESTED):

$string =~ s/ __ (?: [a-zA-Z]_ ){1,2} /__/xms;
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i also assume there is only one instance of the sub-string in a string, and so the  /g regex modifier is not needed. also, that variations on the sub-strings  "__AA_" and  "__AA_AA_" will not occur.

note: more examples would help the humble monks to better understand the requirements.