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That is a heck of an obscure novel, at least to me. Maybe check the book's title to see if articles about "The Master and Margarita" list any literary references, which might mentuon the graphic novel.
Also, look for information on adult graphic novels and see if any details about a plot might ring a bell with you. The good thing is that realistic graphic novels for older reaxers is a relatively new (2000 and later) phenomeon. Good luck!
This is a bit late, but you're probably thinking of Lena Finkle's Magic Barrel by Anya Ulinich.
This was a graphic novel for adults. You know the kind—the sort of thing with the kind of realistic plot that would be a foreign drama if it were a movie. It might have been autobiographical, but I wouldn't swear on it.
I don't remember much, except that at one point the protagonist, who's a woman, discussed The Master and Margarita with a man she knew.